PyMOL Command Reference

This is the list of all PyMOL commands which can be used in the PyMOL command line and in PML scripts. The command descriptions found in this file can also be printed to the PyMOL text buffer with the help command. Example:

PyMOL>help color
...

The list of arguments for a command (the "usage") can be queried on the command line with a questionmark. Example:

PyMOL>color ?
Usage: color color [, selection [, quiet [, flags ]]]

The square brackets ("[" and "]") indicate optional arguments and are not part of the syntax.

If the PyMOL command interpreter doesn't understand some input, it passes it to the Python interpreter. This means that single-line Python expressions can be put into PML scripts or typed into the command line. Prefixing a line with a slash (/) forces the interpreter to pass it to Python. See also the python command to input multi-line Python scripts.

This file can be generated on the PyMOL command line:

PyMOL>cmd.write_html_ref('pymol-command-ref.html')



abort

DESCRIPTION

    "abort" abruptly terminates execution of the PyMOL command script
    without executing any additional commands.

SEE ALSO

    embed, skip, python

api: pymol.helping.abort


accept

DESCRIPTION

    "accept" is an internal method for handling of session file
    security.

api: pymol.moving.accept


alias

DESCRIPTION

    "alias" binds routinely-used command inputs to a new command
    keyword.

USAGE

    alias name, command

ARGUMENTS

    name = string: new keyword
    
    command = string: literal input with commands separated by semicolons.
    
EXAMPLE

    alias my_scene, hide; show ribbon, polymer; show sticks, organic; show nonbonded, solvent
    
    my_scene

NOTES

    For security reasons, aliased commands are not saved or restored
    in sessions.

SEE ALSO

    cmd.extend, api

api: pymol.commanding.alias


align

DESCRIPTION

    "align" performs a sequence alignment followed by a structural
    superposition, and then carries out zero or more cycles of
    refinement in order to reject structural outliers found during
    the fit. "align" does a good job on proteins with decent sequence
    similarity (identity >30%). For comparing proteins with lower
    sequence identity, the "super" and "cealign" commands perform
    better.

USAGE 

    align mobile, target [, cutoff [, cycles
        [, gap [, extend [, max_gap [, object
        [, matrix [, mobile_state [, target_state
        [, quiet [, max_skip [, transform [, reset ]]]]]]]]]]]]]

ARGUMENTS

    mobile = string: atom selection of mobile object

    target = string: atom selection of target object

    cutoff = float: outlier rejection cutoff in Angstrom {default: 2.0}

    cycles = int: maximum number of outlier rejection cycles {default: 5}

    gap, extend, max_gap: sequence alignment parameters

    object = string: name of alignment object to create {default: (no
    alignment object)}

    matrix = string: file name of substitution matrix for sequence
    alignment {default: BLOSUM62}

    mobile_state = int: object state of mobile selection {default: 0 = all states}

    target_state = int: object state of target selection {default: 0 = all states}

    transform = 0/1: do superposition {default: 1}
        
NOTES

    If object is specified, then align will create an object which
    indicates paired atoms and supports visualization of the alignment
    in the sequence viewer.

    The RMSD of the aligned atoms (after outlier rejection!) is reported
    in the text output. The all-atom RMSD can be obtained by setting
    cycles=0 and thus not doing any outlier rejection.

EXAMPLE

    align protA////CA, protB////CA, object=alnAB

SEE ALSO

    super, cealign, pair_fit, fit, rms, rms_cur, intra_rms, intra_rms_cur

api: pymol.fitting.align


alignto

DESCRIPTION

        "alignto" aligns all other loaded objects to the target
        using the specified alignment algorithm.

USAGE

        alignto target [, method [, quiet ]]

NOTES

        Available alignment methods are "align", "super" and "cealign".

EXAMPLE

        # fetch some calmodulins
        fetch 1cll 1sra 1ggz 1k95, async=0

        # align them to 1cll using cealign
        alignto 1cll, method=cealign
        alignto 1cll, object=all_to_1cll

SEE ALSO

        extra_fit, align, super, cealign, fit, rms, rms_cur, intra_fit

api: pymol.fitting.alignto


alphatoall

DESCRIPTION

    Expand any given property of the CA atoms to all atoms in the residue

ARGUMENTS

    selection = string: atom selection {default: polymer}

    properties = string: space separated list of atom properties {default: b}

api: pymol.editing.alphatoall


alter

DESCRIPTION

    "alter" changes atomic properties using an expression evaluated
    within a temporary namespace for each atom.

USAGE

    alter selection, expression

EXAMPLES

    alter chain A, chain='B'
    alter all, resi=str(int(resi)+100)
    sort

NOTES

    Symbols defined (* = read only):

    name, resn, resi, resv, chain, segi, elem, alt, q, b, vdw, type,
    partial_charge, formal_charge, elec_radius, text_type, label, 
    numeric_type, model*, state*, index*, ID, rank, color, ss,
    cartoon, flags

    All strings must be explicitly quoted.  This operation typically
    takes several seconds per thousand atoms altered.  

    You may need to issue a "rebuild" in order to update associated
    representations.
    
    WARNING: You should always issue a "sort" command on an object
    after modifying any property which might affect canonical atom
    ordering (names, chains, etc.).  Failure to do so will confound
    subsequent "create" and "byres" operations.  

SEE ALSO

    alter_state, iterate, iterate_state, sort

api: pymol.editing.alter


alter_state

DESCRIPTION

    "alter_state" changes atom coordinates and flags over a particular
    state and selection using the Python evaluator with a temporary
    namespace for each atomic coordinate.

USAGE

    alter_state state, selection, expression

EXAMPLES

    alter_state 1, all, x=x+5
    rebuild
    
NOTES

    By default, most of the symbols from "alter" are available for use
    on a read-only basis.  

    It is usually necessary to "rebuild" representations once your
    alterations are complete.
    
SEE ALSO

    iterate_state, alter, iterate

api: pymol.editing.alter_state


angle

DESCRIPTION

    "angle" shows the angle formed between any three atoms.

USAGE

    angle [ name [, selection1 [, selection2 [, selection3 ]]]]

NOTES

    "angle" alone will show the angle angle formed by selections (pk1),
    (pk2), (pk3) which can be set using the "PkAt" mouse action
    (typically, Ctrl-middle-click)

PYMOL API

    cmd.angle(string name, string selection1, string selection2,
              string selection3)

SEE ALSO

    distance, dihedral

api: pymol.querying.angle


api

DESCRIPTION

    API helper function. Get the full function name (incl. module) of
    given command.

ARGUMENTS

    name = string: name of a PyMOL command

NOTES

    The PyMOL Python Application Programming Interface (API) should be
    accessed exclusively through the "cmd" module (never "_cmd"!).  Nearly
    all command-line functions have a corresponding API method.

    from pymol import cmd
    result = cmd.<command-name>( argument , ... ) 

    Although the PyMOL core is not multi-threaded, the API is
    thread-safe and can be called asynchronously by external python
    programs.  PyMOL handles the necessary locking to insure that
    internal states do not get corrupted.  This makes it very easy to
    build complicated systems which involve direct realtime visualization.

api: pymol.helping.api


as

DESCRIPTION

    "as" turns on and off atom and bond representations.

USAGE

    as representation [, selection ]

ARGUMENTS
    
    representation = lines, spheres, mesh, ribbon, cartoon, sticks,
        dots, surface, labels, extent, nonbonded, nb_spheres, slice,
        extent, slice, dashes, angles, dihedrals, cgo, cell, callback,
        volume or everything

    selection = string {default: all}

EXAMPLES

    as lines, name CA+C+N

    as ribbon

PYMOL API

    cmd.show_as(string representation, string selection)

NOTES

    "selection" can be an object name
    "as" alone will turn on lines and nonbonded and hide everything else.

SEE ALSO

    show, hide, enable, disable

api: pymol.viewing.show_as


assign_stereo

DESCRIPTION

    Assign "stereo" atom property (R/S stereochemistry).

    Requires either a Schrodinger Suite installation (SCHRODINGER
    environment variable set) or RDKit (rdkit Python module).

USAGE

    assign_stereo [selection [, state [, method ]]]

ARGUMENTS

    selection = str: atom selection {default: all}

    state = int: object state {default: -1 (current)}

    method = schrodinger or rdkit: {default: try both}

api: pymol.stereochemistry.assign_stereo


attach

DESCRIPTION

    "attach" adds a single atom on to the picked atom.

USAGE

    attach element, geometry, valence

PYMOL API

    cmd.attach( element, geometry, valence )

api: pymol.editing.attach


backward

DESCRIPTION

    "backward" moves the movie back one frame.

USAGE

    backward

PYMOL API

    cmd.backward()

SEE ALSO

    mset, forward, rewind

api: pymol.moving.backward


bg_color

DESCRIPTION

    "bg_color" sets the background color.

USAGE

    bg_color [ color ]

ARGUMENTS

    color = string: color name or number {default: black}

EXAMPLES

    bg_color grey30

    bg_color
    
NOTES

    To obtain a transparent background, "unset opaque_background", and
    then use "ray".
    
SEE ALSO

    set_color, ray
    
PYMOL API

    cmd.bg_color(string color)

api: pymol.viewing.bg_color


bond

DESCRIPTION

    "bond" creates a new bond between two selections, each of which
    should contain one atom.

USAGE

    bond [atom1, atom2 [,order]]

NOTES

    The atoms must both be within the same object.

    The default behavior is to create a bond between the (lb) and (rb)
    selections.

PYMOL API

    cmd.bond(string atom1, string atom2)

SEE ALSO

    unbond, fuse, attach, replace, remove_picked

api: pymol.editing.bond


button

DESCRIPTION

    "button" can be used to redefine what the mouse buttons do.

USAGE

    button button, modifier, action

ARGUMENTS

    button = left, middle, right, wheel, double_left, double_middle,
        double_right, single_left, single_middle, or single_right
       
    modifiers = None, Shft, Ctrl, CtSh, CtAl, CtAl, CtAS, 

    actions = None, Rota, Move, MovZ, Slab, +Box, -Box, Clip, MovS,
        +/-, PkAt, Pk1, MvSZ, Sele, Orig, Menu, PkAt, Pk1 RotO, MovO,
        MvOZ, MovA, PkAt, PkTB, MvSZ MvAZ, DrgM, RotZ, PkBd, ClpN,
        ClpF

NOTES

   Changes made using the button command are easily overridden when
   the user iterates through the mouse modes.  This behavior needs to
   be changed.

   Obsolete actions: lb, mb, rb, +lb, +mb, +rb, +lbX, -lbX,
      
   Unsupported, Internal, or Future Actions: RotD, MovD, MvDZ, RotF,
    MovF, MvFZ, TorF, RotV, MovV, MvVZ, DgMZ, DgRT

PYMOL API

    cmd.button(string button, string modifier, string action)

SEE ALSO

    config_mouse

api: pymol.controlling.button


cache

DESCRIPTION

    "cache" manages storage of precomputed results, such as
    molecular surfaces.

USAGE

    cache action [, scenes [, state ]]

ARGUMENTS

    action = string: enable, disable, read_only, clear, or optimize

    scenes = string: a space-separated list of scene names (default: '')

    state = integer: state index (default: -1)

EXAMPLES

    cache enable
    cache optimize
    cache optimize, F1 F2 F5

NOTES

    "cache optimize" will iterate through the list of scenes provided
    (or all defined scenes), compute any missing surfaces, and store
    them in the cache for later reuse.
    
PYMOL API

    cmd.cache(string action, string scenes, int state, int quiet)

api: pymol.exporting.cache


callout

DESCRIPTION

    Create a new screen-stabilized callout object.

ARGUMENTS

    name = str: object name

    label = str: label text

    pos = str or list: anchor in model space as 3-float coord list or atom
    selection. If empty, don't draw an arrow. {default: }

    screen = str or list: position on screen as 2-float list between [-1,-1]
    (lower left) and [1,1] (upper right) or "auto" for smart placement.
    {default: auto}

api: pymol.experimenting.callout


capture

UNDOCUMENTED

api: pymol.viewing.capture


cartoon

DESCRIPTION

    "cartoon" changes the default cartoon representation for a set of atoms.

USAGE

    cartoon type, selection

ARGUMENTS

    type = automatic, skip, loop, rectangle, oval, tube, arrow, dumbbell
    
PYMOL API

    cmd.cartoon(string type, string selection)

EXAMPLES

    cartoon rectangle, chain A

    cartoon skip, resi 145-156

NOTES

    This command is rarely required since the default "automatic" mode
    chooses cartoons according to the information in the PDB HELIX and
    SHEET records.

api: pymol.viewing.cartoon


cd

DESCRIPTION

    "cd" changes the current working directory.

USAGE

    cd <path>

SEE ALSO

    pwd, ls, system

api: pymol.externing.cd


cealign

DESCRIPTION

    "cealign" aligns two proteins using the CE algorithm.

USAGE 

    cealign target, mobile [, target_state [, mobile_state [, quiet [,
        guide [, d0 [, d1 [, window [, gap_max, [, transform ]]]]]]]]]

NOTES

    If "guide" is set PyMOL will align using only alpha carbons, which is the
    default behavior. Otherwise, PyMOL will use all atoms. If "quiet" is set
    to -1, PyMOL will print the rotation matrix as well.

    Reference: Shindyalov IN, Bourne PE (1998) Protein structure alignment by
    incremental combinatorial extension (CE) of the optimal path.  Protein
    Engineering 11(9) 739-747.

EXAMPLES

    cealign protA////CA, protB////CA

    # fetch two proteins and align them
    fetch 1rlw 1rsy, async=0
    cealign 1rlw, 1rsy

SEE ALSO

    align, pair_fit, fit, rms, rms_cur, intra_rms, intra_rms_cur, super

api: pymol.fitting.cealign


center

DESCRIPTION

    "center" translates the window, the clipping slab, and the
    origin to a point centered within the atom selection.

USAGE

    center [ selection [, state [, origin [, animate ]]]]

EXAMPLES

    center chain B
    center 145/

ARGUMENTS

    selection = string: selection-expression or name pattern (default: "all").
    
    state = 0 (default) use all coordinate states
    
    state = -1 use only coordinates for the current state
    
    state > 0  use coordinates for a specific state

    origin = 1 (default) move the origin
    
    origin = 0 leave the origin unchanged

PYMOL API

    cmd.center(string selection, int state, int origin)

SEE ALSO

    origin, orient, zoom

api: pymol.viewing.center


centerofmass

DESCRIPTION

    Calculates the center of mass. Considers atom mass and occupancy.

ARGUMENTS

    selection = string: atom selection {default: all}

    state = integer: object state, -1 for current state, 0 for all states
    {default: -1}

NOTES

    If occupancy is 0.0 for an atom, set it to 1.0 for the calculation
    (assume it was loaded from a file without occupancy information).

SEE ALSO

    get_extent

api: pymol.querying.centerofmass


check

DESCRIPTION

    "check" is unsupported command that may eventually have something
    to do with assigning forcefield parameters to a selection of
    atoms.

api: pymol.experimenting.check


clean

DESCRIPTION

    Note: This operation is limited to 999 atoms.

    Run energy minimization on the given selection, using an MMFF94
    force field.

ARGUMENTS

    selection = str: atom selection to minimize

    present = str: selection of fixed atoms to restrain the minimization

    state = int: object state {default: -1 (current)}

    fix = UNUSED

    restraing = UNUSED

    method = UNUSED

    async = 0/1: run in separate thread {default: 0}

    save_undo = UNUSED

    message = Message to display during async minimization

EXAMPLE

    # minimize ligand in binding pocket
    clean organic, all within 8 of organic

api: pymol.computing.clean


clip

DESCRIPTION

    "clip" alters the positions of the clipping planes.

USAGE

    clip mode, distance [, selection [, state ]]

ARGUMENTS 

    mode = near, far, move, slab, or atoms

    distance is a floating point value

    selection = atom selection (for mode=atoms only)

EXAMPLES

    clip near, -5           # moves near plane away from you by 5 A
    clip far, 10            # moves far plane towards you by 10 A
    clip move, -5           # moves the slab away from you by 5 A
    clip slab, 20           # sets slab thickness to 20 A
    clip slab, 10, resi 11  # clip 10 A slab about residue 11

    clip atoms, 5, pept     # clip atoms in "pept" with a 5 A buffer
                            # about their current camera positions

PYMOL API

    cmd.clip(string mode, float distance, string selection, int state)

SEE ALSO

    zoom, orient, reset

api: pymol.viewing.clip


cls

DESCRIPTION

    "cls" clears the output buffer.

USAGE

    cls

api: pymol.commanding.cls


color

DESCRIPTION

    "color" changes the color of objects or atoms.

USAGE

    color color [, selection ]

ARGUMENTS

    color = string: color name or number

    selection = string: selection-expression or name-pattern
    corresponding to the atoms or objects to be colored
    {default: (all)}.

NOTES

    When using color ramps, the ramp can be used as a color.
    
PYMOL API

    cmd.color(string color, string selection, int quiet)

SEE ALSO

    set_color, recolor
    
EXAMPLE 

    color cyan
    color yellow, chain A

api: pymol.viewing.color


conda

DESCRIPTION

    Experimental and limited conda wrapper for PyMOL bundles. Automatically
    passes "--yes" to "conda install".

EXAMPLE

    conda install biopython

api: pymol.externing.conda


config_mouse

DESCRIPTION

    "config_mouse" sets the current mouse configuration ring.

USAGE

    config_mouse ring

EXAMPLES

    config_mouse three_button
    config_mouse two_button
    config_mouse one_button
    
PYMOL API

    cmd.config_mouse(string ring, int quiet)

SEE ALSO

    mouse, button

api: pymol.controlling.config_mouse


copy

DESCRIPTION

    "copy" creates a new object that is an identical copy of an
    existing object.

USAGE

    copy target, source [, zoom ]

NOTES

    Currently, this command only works for molecular objects.

SEE ALSO

    create

api: pymol.creating.copy


copy_to

DESCRIPTION

    Copies selection to object `name` (all states) and by default
    renames chain, segi and ID identifiers to avoid naming conflicts.

ARGUMENTS

    name = str: object name to modify

    selection = str: atom selection (will be copied to `name`)

    rename = str: space separated list of identifiers to rename
    {default: chain segi ID}

SEE ALSO

    create, fuse

api: pymol.editing.copy_to


count_atoms

DESCRIPTION

    "count_atoms" returns a count of atoms in a selection.

USAGE

    count_atoms [ selection [, quiet [, state ]]]

api: pymol.querying.count_atoms


count_discrete

DESCRIPTION

    Count the number of discrete objects in selection.

USAGE

    count_discrete selection

api: pymol.querying.count_discrete


count_frames

DESCRIPTION

    "count_frames" returns the number of frames defined for the PyMOL
    movie.

USAGE

    count_frames
    
PYMOL API

    cmd.count_frames()

SEE ALSO

    frame, count_states

api: pymol.querying.count_frames


count_states

DESCRIPTION

    "count_states" returns the number of states in the selection.

USAGE

    count_states
    
PYMOL API

    cmd.count_states(string selection)

SEE ALSO

    frame

api: pymol.querying.count_states


create

DESCRIPTION

    "create" creates a new molecule object from a selection.  It can
    also be used to create states in an existing object.

USAGE

    create name, selection [,source_state [,target_state ] ]

ARGUMENTS

    name = string: name of object to create or modify

    selection = string: atoms to include in the new object

    source_state = integer: {default: 0 -- copy all states}

    target_state = integer: -1 appends after last state {default: 0}

    copy_properties = boolean: {default: False} copies properties from source
                               (last of the same properties survives with multiple objects)

PYMOL API

    cmd.create(string name, string selection, int state,
               int target_state, int discrete)

NOTES

    If the source and target states are zero (default), then all
    states will be copied.  Otherwise, only the indicated states will
    be copied.

SEE ALSO

    load, copy, extract

api: pymol.creating.create


cycle_valence

DESCRIPTION

    "cycle_valence" cycles the valence on the currently selected bond.

USAGE

    cycle_valence [ h_fill ]

ARGUMENTS

    h_fill = 0 or 1: updated hydrogens too? {default: 1 (yes)}
    
EXAMPLE

    cycle_valence

NOTES

    If the h_fill flag is true, hydrogens will be added or removed to
    satisfy valence requirements.

    This function is usually connected to the DELETE key and "CTRL-W".

PYMOL API

    cmd.cycle_valence(int h_fill)

SEE ALSO

    remove_picked, attach, replace, fuse, h_fill

api: pymol.editing.cycle_valence


decline

DESCRIPTION

    "decline" is an internal method for handling of session file
    security.

api: pymol.moving.decline


delete

DESCRIPTION

    "delete" removes objects and named selections

USAGE

    delete name

ARGUMENTS

    name = name(s) of object(s) or selection(s), supports wildcards (*)

EXAMPLES

    delete measure*     # delete all objects which names start with "measure"
    delete all          # delete all objects and selections

PYMOL API

    cmd.delete (string name = object-or-selection-name )

SEE ALSO

    remove

api: pymol.commanding.delete


deprotect

DESCRIPTION

    "deprotect" reverses the effect of the "protect" command.

USAGE

    deprotect (selection)

PYMOL API

    cmd.deprotect(string selection)

SEE ALSO

    protect, mask, unmask, mouse, editing

api: pymol.editing.deprotect


desaturate

DESCRIPTION

    Desaturate the colors in the given selection.

ARGUMENTS

    selection = str: atom selection {default: all}

    a = float [0..1]: desaturation factor {default: 0.5}

api: pymol.experimenting.desaturate


deselect

DESCRIPTION

    "deselect" disables any and all visible selections

USAGE

    deselect

PYMOL API

    cmd.deselect()

api: pymol.selecting.deselect


diagnostics

DESCRIPTION

    Get system level diagnostics data

USAGE

    diagnostics [ filename ]

ARGUMENTS

    filename = str: If given, write output to text file

api: pymol.diagnosing.diagnostics


dihedral

DESCRIPTION

    "dihedral" shows dihedral angles formed between any four atoms.

USAGE

    dihedral [ name [, selection1 [, selection2 [, selection3 [, selection4 ]]]]]


NOTES

    "dihedral" alone will show the dihedral angle formed by selections
    (pk1), (pk2), (pk3), and (pk4), which can be set using the "PkAt"
    mouse action (typically, Ctrl-middle-click)

PYMOL API

    cmd.dihedral(string name, string selection1, string selection2,
                 string selection3, string selection4)

SEE ALSO

    distance, angle

api: pymol.querying.dihedral


dir

DESCRIPTION

    List contents of the current working directory.

USAGE

    ls [pattern]
    dir [pattern]

EXAMPLES

    ls
    ls *.pml

SEE ALSO

    cd, pwd, system

api: pymol.externing.ls


disable

DESCRIPTION

    "disable" turns off display of one or more objects and/or selections.

USAGE

    disable name

ARGUMENTS    

    name = name-pattern or selection.

PYMOL API

    cmd.disable(string name) 

SEE ALSO

    show, hide, enable

api: pymol.viewing.disable


distance

DESCRIPTION

    "distance" creates a new distance object between two selections.

USAGE
    
    distance [name [, selection1 [, selection2 [, cutoff [, mode ]]]]]

ARGUMENTS

    name = string: name of the distance object to create

    selection1 = string: first atom selection

    selection2 = string: second atom selection

    cutoff = float: longest distance to show 
    
    mode = 0: all interatomic distances

    mode = 1: only bond distances

    mode = 2: only show polar contact distances

    mode = 3: like mode=0, but use distance_exclusion setting

    mode = 4: distance between centroids (does not support
              dynamic_measures; new in PyMOL 1.8.2)

    state = int: object state to create the measurement object in
    and to get coordinates from {default: 0 (all states)}

    state1, state2 = int: overrule 'state' argument to measure distances
    between different states {default: use state}

EXAMPLES

    distance mydist, 14/CA, 29/CA

    distance hbonds, all, all, 3.2, mode=2

NOTES

    The distance wizard makes measuring distances easier than using
    the "dist" command for real-time operations.

    "dist" alone will show distances between selections (pk1) and (pk1),
    which can be set using the PkAt mouse action (usually CTRL-middle-click).

PYMOL API

    cmd.distance(string name, string selection1, string selection2,
                 string cutoff, string mode )

api: pymol.querying.distance


drag

DESCRIPTION

    "drag" activates dragging for a selection, enabling the user to
    manipulate the atom coordinates of the atoms using mouse controls
    similar to those for controlling the camera.

USAGE

    drag [ selection ]

ARGUMENTS
  
    selection = string: atoms to drag.  If not provided, and dragging
    is active, then dragging is instead deactivated.

NOTES

    Currently, the selection of atom to drag must all reside in a
    single molecular object.

api: pymol.editing.drag


draw

DESCRIPTION

    "draw" creates an OpenGL-based image of the current frame.  

USAGE

    draw [width [,height [,antialias ]]]

ARGUMENTS

    width = integer {default: 0 (current)}

    height = integer {default: 0 (current)}

    antialias = integer {default: -1 (use antialias setting)}
    
EXAMPLES

    draw
    draw 1600

NOTES

    Default width and height are taken from the current viewpoint. If
    one is specified but not the other, then the missing value is
    scaled so as to preserve the current aspect ratio.

    Because this feature uses the OpenGL rendering context to piece
    together the image, it does not work when running in the
    command-line only mode.

    On certain graphics hardware, "unset opaque_background" followed
    by "draw" will produce an image with a transparent background.
    However, better results can usually be obtained using "ray".
    
PYMOL API

    cmd.draw(int width, int height, int antialias, int quiet)

SEE ALSO

    ray, png, save

api: pymol.viewing.draw


dss

DESCRIPTION

    "dss" defines secondary structure based on backbone geometry
    and hydrogen bonding patterns.
    
USAGE

    dss selection, state

ARGUMENT

    selection = string: {default: (all)}

    state = integer: {default: 0 -- all states}
    
EXAMPLE

    dss

NOTES

    With PyMOL, heavy emphasis is placed on cartoon aesthetics, and so
    both hydrogen bonding patterns and backbone geometry are used in
    the assignment process.  Depending upon the local context, helix
    and strand assignments are made based on geometry, hydrogen
    bonding, or both.

    This command will generate results which differ slightly from DSSP
    and other programs.  Most deviations occur in borderline or
    transition regions.  Generally speaking, PyMOL is more strict, thus
    assigning fewer helix/sheet residues, except for partially
    distorted helices, which PyMOL tends to tolerate.
    
    WARNING: This algorithm has not yet been rigorously validated.

    If you dislike one or more of the assignments made by dss, you can
    use the alter command to make changes (followed by "rebuild").
    For example:
    
        alter 123-125/, ss='L'
        alter pk1, ss='S'
        alter 90/, ss='H'
        rebuild

PYMOL API

    cmd.dss(string selection, int state)

api: pymol.editing.dss


dump

DESCRIPTION

    "dump" is an unsupported command which may have something to do
    with outputing isosurface meshes and surface objects to a file.

api: pymol.experimenting.dump


edit

DESCRIPTION

    "edit" picks atoms or a bond for editing.

USAGE

    edit selection1 [, selection2 [, selection3 [, selection4 [, pkresi [, pkbond ]]]]] 

NOTES

    If only one selection is provided, an atom is picked.

    If two selections are provided, the bond between them
    is picked (by default, if one exists).

PYMOL API

    cmd.edit(string selection1, string selection2,
             string selection3, string selection4,
             int pkresi, int pkbond, int quiet)

SEE ALSO

    unpick, remove_picked, cycle_valence, torsion

api: pymol.editing.edit


edit_mode

DESCRIPTION

    "edit_mode" switches the mouse into editing mode, if such a mode
    is available in the current mouse ring.

api: pymol.controlling.edit_mode


embed

DESCRIPTION

    "embed" delimits a block of data embedded in a PyMOL command
    script.

USAGE

    embed key [, type [, sentinel ]]

ARGUMENTS

    key = string: unique indentifier for the data

    type = pdb, mol, mol2, sdf, xplor

    sentinel = string: a unique string signalling the end of the data {default: embed end}
    
EXAMPLE

    embed wats, pdb
    HETATM    1  O   WAT     1       2.573  -1.034  -1.721
    HETATM    2  H1  WAT     1       2.493  -1.949  -1.992
    HETATM    3  H2  WAT     1       2.160  -0.537  -2.427
    HETATM    4  O   WAT     2       0.705   0.744   0.160
    HETATM    5  H1  WAT     2      -0.071   0.264   0.450
    HETATM    6  H2  WAT     2       1.356   0.064  -0.014
    embed end
    
NOTES

    Only text data formats can be used with embed
    
SEE ALSO

    abort, skip, python

api: pymol.helping.embed


enable

DESCRIPTION

    "enable" turns on display of one or more objects and/or selections.

USAGE

    enable name

ARGUMENTS    

    name = name-pattern or selection. 

NOTES

    If name matches a selection name, then selection indicator dots
    are shown for atoms in that selection.  If name is a
    selection-expression, then all objects with atoms in that
    selection are enabled.

    For an object's content to be displayed in the 3D viewer, the
    object must be enabled AND at least one of the available
    representations must be shown.
    
PYMOL API

    cmd.enable(string object-name)

EXAMPLES

    enable target_protein  # enables the target_protein object

    enable 1dn2.*   # enables all entities starting with 1dn2.
    
    enable *lig     # enables all entities ending with lig
    
SEE ALSO

    show, hide, disable

api: pymol.viewing.enable


ending

DESCRIPTION

    "ending" goes to the end of the movie.

USAGE

    ending

PYMOL API

    cmd.ending()

api: pymol.moving.ending


export_dots

DESCRIPTION

    "export_dots" is an old unsupported command that may have
    something to do with returning the coordinates of the dot
    representation back to the Python layer.

api: pymol.querying.export_dots


extra_fit

DESCRIPTION

    Like "intra_fit", but for multiple objects instead of
    multiple states.

ARGUMENTS

    selection = string: atom selection of multiple objects {default: all}

    reference = string: reference object name {default: first object in selection}

    method = string: alignment method (command that takes "mobile" and "target"
    arguments, like "align", "super", "cealign" {default: align}

    ... extra arguments are passed to "method"

SEE ALSO

    align, super, cealign, intra_fit, util.mass_align

api: pymol.fitting.extra_fit


extract

DESCRIPTION

    "extract" is simply a shorthand way calling the "create" command
    with the extract argument activated, so that atoms in the new
    object are removed from the source object.

USAGE

    extract name, selection [, source_state [, target_state ]]

SEE ALSO

    create

api: pymol.creating.extract


fab

DESCRIPTION

    Build a peptide

ARGUMENTS

    input = str: sequence in one-letter code

    name = str: name of object to create {default: }

    ss = int: Secondary structure 1=alpha helix, 2=antiparallel beta, 3=parallel beta, 4=flat

EXAMPLE

    fab ACDEFGH
    fab ACDEFGH, helix, ss=1

api: pymol.editor.fab


feedback

DESCRIPTION

    "feedback" changes the amount of information output by pymol.

USAGE

    feedback action, module, mask

ARGUMENTS

    action = set, enable, or disable

    module = string: a space-separated list of modules or simply "all"

    mask = string: a space-separated list of output categories or simply "everything"

NOTES

    "feedback" alone will print a list of the available module choices

PYMOL API

    cmd.feedback(string action,string module,string mask)

EXAMPLES

    feedback enable, all , debugging
    feedback disable, selector, warnings actions
    feedback enable, main, blather

api: pymol.feedingback.feedback


fetch

DESCRIPTION

    "fetch" downloads a file from the internet (if possible)

USAGE

    fetch code [, name [, state [, finish [, discrete [, multiplex
        [, zoom [, type [, async [, path ]]]]]]]]]

ARGUMENTS

    code = a single PDB identifier or a list of identifiers. Supports
    5-letter codes for fetching single chains (like 1a00A).

    name = the object name into which the file should be loaded.

    state = the state number into which the file should loaded.

    type = str: cif, pdb, pdb1, 2fofc, fofc, emd, cid, sid {default: cif
    (default was "pdb" up to 1.7.6)}

    async_ = 0/1: download in the background and do not block the PyMOL
    command line {default: 0 -- changed in PyMOL 2.3}

PYMOL API

    cmd.fetch(string code, string name, int state, init finish,
              int discrete, int multiplex, int zoom, string type,
              int async, string path, string file, int quiet)
              
NOTES

    When running in interactive mode, the fetch command loads
    structures asyncronously by default, meaning that the next command
    may get executed before the structures have been loaded.  If you
    need synchronous behavior in order to insure that all structures
    are loaded before the next command is executed, please provide the
    optional argument "async=0".

    Fetch requires a direct connection to the internet and thus may
    not work behind certain types of network firewalls.

api: pymol.importing.fetch


fit

DESCRIPTION

    "fit" superimposes the model in the first selection on to the model
    in the second selection. Only matching atoms in both selections will
    be used for the fit.
	
USAGE

    fit mobile, target [, mobile_state [, target_state [, quiet
        [, matchmaker [, cutoff [, cycles [, object ]]]]]]]

ARGUMENTS

    mobile = string: atom selection

    target = string: atom selection

    mobile_state = integer: object state {default=0, all states)

    target_state = integer: object state {default=0, all states)

    matchmaker = integer: how to match atom pairs {default: 0}
        -1:  assume that atoms are stored in the identical order
        0/1: match based on all atom identifiers (segi,chain,resn,resi,name,alt)
        2:   match based on ID
        3:   match based on rank
        4:   match based on index (same as -1 ?)

    cutoff = float: outlier rejection cutoff (only if cycles>0) {default: 2.0}

    cycles = integer: number of cycles in outlier rejection refinement {default: 0}

    object = string: name of alignment object to create {default: None}

EXAMPLES

	fit protA, protB

NOTES

	Since atoms are matched based on all of their identifiers
	(including segment and chain identifiers), this command is only
	helpful when comparing very similar structures.

SEE ALSO

	align, super, pair_fit, rms, rms_cur, intra_fit, intra_rms, intra_rms_cur

api: pymol.fitting.fit


fix_chemistry

DESCRIPTION
   
    "fix chemistry" is an unsupported feature.

api: pymol.editing.fix_chemistry


flag

DESCRIPTION

    "flag" sets the indicated flag for atoms in the selection and
     clears the indicated flag for atoms not in the selection.  

USAGE

    flag flag, selection [, action ]

ARGUMENTS

    action = reset: {default} set flag for atoms in selection and clear it for all others

    action = set: set the flag for atoms in selection, leaving other atoms unchanged

    action = clear: clear the flag for selected atoms, leaving other atoms unchanged

EXAMPLES  

    flag free, (resi 45 x; 6)

NOTES

    This is primarily useful for passing selection information into
    Chempy models, which have a 32 bit attribute "flag" which holds
    this information.

    If the 'auto_indicate_flags' setting is true, then PyMOL will automatically
    create a selection called "indicate" which contains all atoms with that flag
    after applying the command.

    SPECIAL FLAGS

    * Flags 0-5 are reserved for molecular modeling

        focus      0 = Atoms of Interest (i.e. a ligand in an active site) \
        free       1 = Free Atoms (free to move subject to a force-field) \
        restrain   2 = Restrained Atoms (typically harmonically contrained) \
        fix        3 = Fixed Atoms (no movement allowed) \
        exclude    4 = Atoms which should not be part of any simulation
        study      5

    * Flags 6-7 are for protein and nucleic acid classification

    * Flags 8-15 are free for end users to manipulate

    * Flags 16-21 are reserved for external GUIs and linked applications

    * Flags 22-23 are for temporary use only (flag 23 used for coverage
      tracking when assigning parameters in chempy.champ.assign)

    * Flags 24-31 are reserved for PyMOL internal usage

        exfoliate 24 = Remove surface from atoms when surfacing \
        ignore    25 = Ignore atoms altogether when surfacing \
        no_smooth 26 = Do not smooth atom position

PYMOL API

    cmd.flag(int flag, string selection, string action="reset",
             int indicate=0)

api: pymol.editing.flag


fnab

DESCRIPTION

    Builds a nucleotide acid from sequence

USAGE

    fnab input [, name [, type [, form [, dbl_helix ]]]]

ARGUMENTS

    input = str: Sequence as an array of one letter codes

    name = str: Name of the object to create {default: obj}

    mode = str: "DNA" or "RNA"

    form = str: "A" or "B"

    dbl_helix = bool (0/1): flag for using double helix in DNA

EXAMPLE

    fnab ATGCGATAC
    fnab ATGCGATAC, name=myDNA, mode=DNA, form=B, dbl_helix=1
    fnab AAUUUUCCG, mode=RNA

api: pymol.editor.fnab


focal_blur

DESCRIPTION

    Creates fancy figures by introducing a focal blur to the image.
    The object at the origin will be in focus.

USAGE

    focal_blur [ aperture [, samples [, ray [, filename ]]]]

ARGUMENTS

    aperture = float: aperture angle in degrees {default: 2.0}

    samples = int: number of images for averaging {default: 10}

    ray = 0/1: {default: 0}

    filename = str: write image to file {default: temporary}

AUTHORS

    Jarl Underhaug, Jason Vertrees and Thomas Holder

EXAMPLES

    focal_blur 3.0, 50

api: pymol.experimenting.focal_blur


fork

DESCRIPTION

    "spawn" launches a Python script in a new thread which will run
    concurrently with the PyMOL interpreter. It can be run in its own
    namespace (like a Python module, default), a local name space, or
    in the global namespace.

USAGE

    spawn file [, namespace ]

NOTES

    The default namespace for spawn is "module".

    The best way to spawn processes at startup is to use the -l option
    (see "help launching").

SEE ALSO

    run

api: pymol.parsing.spawn


forward

DESCRIPTION

    "forward" moves the movie one frame forward.

USAGE

    forward

PYMOL API

    cmd.forward()

SEE ALSO

    mset, backward, rewind

api: pymol.moving.forward


fragment

DESCRIPTION

    "fragment" retrieves a 3D structure from the fragment library,
    which is currently pretty meager (just amino acids).

USAGE

    fragment name

api: pymol.creating.fragment


frame

DESCRIPTION

    "frame" sets the viewer to the indicated movie frame.

USAGE

    frame frame

ARGUMENTS

    frame = integer: frame number to display

EXAMPLE

    frame 10
    
PYMOL API

    cmd.frame( int frame_number )

NOTES

    Frame numbers are 1-based.

SEE ALSO

    count_states

api: pymol.moving.frame


full_screen

DESCRIPTION

    "full_screen" enables or disables full screen mode.  

USAGE

    full_screen [toggle]

EXAMPLES


    full_screen
    full_screen on
    full_screen off

NOTES

    This does not work correctly on all platforms.  If you encounter
    trouble, try using the maximize button on the viewer window
    instead.

api: pmg_qt.pymol_qt_gui.full_screen


fuse

DESCRIPTION

    "fuse" joins two objects into one by forming a bond.  A copy of
    the object containing the first atom is moved so as to form an
    approximately resonable bond with the second, and that copy is
    then merged with the first object.

USAGE

    fuse [ selection1 [, selection2 [, mode [, recolor [, move ]]]]]

ARGUMENTS

    selection1 = str: single atom selection (will be copied to object 2)

    selection2 = str: single atom selection

    mode = int: {default: 0}
      3: don't move and don't create a bond, just combine into single object

    recolor = bool: recolor C atoms to match target {default: 1}

    move = bool: {default: 1}

NOTES

    Each selection must include a single atom in each object.
    The atoms can both be hydrogens, in which case they are
    eliminated, or they can both be non-hydrogens, in which
    case a bond is formed between the two atoms.

SEE ALSO

    bond, unbond, attach, replace, fuse, remove_picked

api: pymol.editing.fuse


get

DESCRIPTION

    "get" prints out the current value of a setting.

USAGE

    get name [, selection [, state ]]
    
EXAMPLE

    get line_width

ARGUMENTS

    name = string: setting name

    selection = string: object name (selections not yet supported)

    state = integer: state number
    
NOTES

    "get" currently only works with global, per-object, and per-state
    settings.  Atom level settings get be queried with "iterate" (e.g.
    iterate all, print s.line_width)
    
PYMOL API

    cmd.get(string name, string object, int state, int quiet)

SEE ALSO

    set, set_bond, get_bond

api: pymol.setting.get


get_angle

DESCRIPTION

    "get_angle" returns the angle between three atoms.  By default, the
    coordinates used are from the current state, however an alternate
    state identifier can be provided.

USAGE

    get_angle atom1, atom2, atom3, [,state ]

EXAMPLES

    get_angle 4/n,4/c,4/ca
    get_angle 4/n,4/c,4/ca,state=4

PYMOL API

    cmd.get_angle(atom1="pk1",atom2="pk2",atom3="pk3",state=-1)

api: pymol.querying.get_angle


get_area

DESCRIPTION

    Get the surface area of an selection. Depends on the "dot_solvent"
    setting. With "dot_solvent=off" (default) it calculates the solvent
    excluded surface area, else the surface accessible surface.

USAGE

    get_area [ selection [, state [, load_b ]]]

ARGUMENTS

    load_b = bool: store per-atom surface area in b-factors {default: 0}

SEE ALSO

    "dot_solvent" setting, "dots" representation (show dots)

api: pymol.querying.get_area


get_bond

DESCRIPTION

    "get_bond" gets per-bond settings for all bonds which exist
    between two selections of atoms.

USAGE

    get_bond name, selection1 [, selection2 ]

ARGUMENTS

    name = string: name of the setting

    selection1 = string: first set of atoms

    selection2 = string: seconds set of atoms {default: (selection1)}

EXAMPLE

    get_bond stick_transparency, */n+c+ca+o


NOTES

    The following per-bond settings are currently implemented.  Others
    may seem to be recognized but will currently have no effect when
    set at the per-bond level.
    
    * valence
    * line_width
    * line_color
    * stick_radius
    * stick_color
    * stick_transparency

PYMOL API

    cmd.get_bond ( string name,
                   string selection1,
                   string selection2,
                   int state, int updates, quiet=1)

api: pymol.setting.get_bond


get_chains

DESCRIPTION

    Print the list of chain identifiers in the given selection.

USAGE

    get_chains [ selection [, state ]]

ARGUMENTS

    selection = str: atom selection {default: all}

    state = int: CURRENTLY IGNORED

api: pymol.querying.get_chains


get_dihedral

DESCRIPTION

    "get_dihedral" returns the dihedral angle between four atoms.  By
    default, the coordinates used are from the current state, however
    an alternate state identifier can be provided.

    By convention, positive dihedral angles are right-handed
    (looking down the atom2-atom3 axis).

USAGE

    get_dihedral atom1, atom2, atom3, atom4 [,state ]

EXAMPLES

    get_dihedral 4/n,4/c,4/ca,4/cb
    get_dihedral 4/n,4/c,4/ca,4/cb,state=4

PYMOL API

    cmd.get_dihedral(atom1,atom2,atom3,atom4,state=-1)

api: pymol.querying.get_dihedral


get_distance

DESCRIPTION

    "get_distance" returns the distance between two atoms.  By default, the
    coordinates used are from the current state, however an alternate
    state identifier can be provided.

USAGE

    get_distance atom1, atom2, [,state ]

EXAMPLES

    get_distance 4/n,4/c
    get_distance 4/n,4/c,state=4
    
PYMOL API

    cmd.get_distance(atom1="pk1",atom2="pk2",state=-1)

api: pymol.querying.get_distance


get_extent

DESCRIPTION

    "get_extent" returns the minimum and maximum XYZ coordinates of a
    selection as an array:
     [ [ min-X , min-Y , min-Z ],[ max-X, max-Y , max-Z ]]

PYMOL API

    cmd.get_extent(string selection="(all)", state=0 )

api: pymol.querying.get_extent


get_position

DESCRIPTION

    "get_position" returns the 3D coordinates of the center of the
    viewer window.

api: pymol.querying.get_position


get_property

DESCRIPTION

    Get an object-level property

ARGUMENTS

    propname = string: Name of the property

    name = string: Name of a single object

    state = int: Object state, 0 for all states, -1 for current state
    {default: 0}

api: pymol.properties.get_property


get_property_list

DESCRIPTION

    Get all properties for an object (for a particular state) as a list

ARGUMENTS

    object = string: Name of a single object

    state = int: Object state, 0 for all states, -1 for current state
    {default: 0}

api: pymol.properties.get_property_list


get_renderer

DESCRIPTION

    Prints OpenGL renderer information.

api: pymol.querying.get_renderer


get_sasa_relative

DESCRIPTION

    Calculates the relative per-residue solvent accessible surface area
    and optionally labels and colors residues. The value is relative to
    full exposure of the residue, calculated by removing all other
    residues except its two next neighbors, if present.

    Loads a value beteween 0.0 (fully buried) and 1.0 (fully exposed)
    into the b-factor property, available in "iterate", "alter" and
    "label" as "b".

USAGE

    get_sasa_relative [ selection [, state [, vis [, var ]]]]

ARGUMENTS

    selection = str: atom selection {default: all}

    state = int: object state {default: 1}

    vis = 0/1: show labels and do color by exposure {default: !quiet}

    var = str: name of property to assign {default: b}

    quiet = 0/1: print results to log window

    outfile = str: filename, write to file instead of log window {default: }

EXAMPLE

    fetch 1ubq, async=0
    get_sasa_relative polymer

PYTHON API

    cmd.get_sasa_relative(...) -> dict

SEE ALSO

    get_area with "load_b=1" argument.

api: pymol.util.get_sasa_relative


get_symmetry

DESCRIPTION

    "get_symmetry" can be used to obtain the crystal
    and spacegroup parameters for a molecule or map.

USAGE

    get_symmetry object-name-or-selection

PYMOL API

    cmd.get_symmetry(string selection, int state, int quiet)

api: pymol.querying.get_symmetry


get_title

DESCRIPTION

    "get_title" retrieves a text string to the state of a particular
    object which will be displayed when the state is active.

USAGE

    set_title object, state

PYMOL API

    cmd.set_title(string object, int state, string text)

api: pymol.querying.get_title


get_type

DESCRIPTION

    "get_type" returns a string describing the named object or
     selection or the string "nonexistent" if the name in unknown.

PYMOL API

    cmd.get_type(string object-name)

NOTES

    Possible return values are

    "object:molecule"
    "object:map"
    "object:mesh"
    "object:slice"
    "object:surface"
    "object:measurement"
    "object:cgo"
    "object:group"
    "object:volume"
    "selection"

SEE ALSO

    get_names

api: pymol.querying.get_type


get_version

DESCRIPTION
 
    "get_version" returns a tuple of length six containing text,
    floating point, and integer representations of the current PyMOL
    version number, build date as unix timestamp, GIT SHA and SVN
    code revision so far available.
   
PYMOL API

    cmd.get_version(int quiet)

api: pymol.querying.get_version


get_view

DESCRIPTION

    "get_view" returns and optionally prints out the current view
    information in a format which can be embedded into a command
    script and can be used in subsequent calls to "set_view".

    If a log file is currently open, get_view will not write the view
    matrix to the screen unless the "output" parameter is 2.

USAGE

    get_view [output]

ARGUMENTS

    output = 0: output matrix to screen

    output = 1: do not Output matrix to screen

    output = 2: force output to screen even if log file is open

    output = 3: return formatted string instead of a list

NOTES

    Contents of the view matrix:
    
    * 0  -  8: column-major 3x3 matrix which rotates model space to camera space

    * 9  - 11: origin of rotation relative to camera (in camera space)

    * 12 - 14: origin of rotation (in model space)

    * 15: front plane distance from the camera

    * 16: rear plane distance from the camera

    * 17: orthoscopic flag (+/-) and field of view (if abs(value) > 1)

    The camera always looks down -Z with its +X left and its +Y down.

    Therefore, in the default view, model +X is to the observer's
    right, +Y is upward, and +Z points toward the observer.

PYMOL API

    cmd.get_view(output=1, quiet=1)

SEE ALSO

    set_view

api: pymol.viewing.get_view


get_viewport

DESCRIPTION

    "get_viewport" returns and optionally prints out the screen viewport size

    If a log file is currently open, get_viewport will not write the view
    matrix to the screen unless the "output" parameter is 2.

USAGE

    get_viewport [output]

ARGUMENTS

    output = 0: output matrix to screen

    output = 1: do not Output matrix to screen

    output = 2: force output to screen even if log file is open

    output = 3: return formatted string instead of a list

PYMOL API

    cmd.get_viewport(output=1, quiet=1)

api: pymol.viewing.get_viewport


gradient

DESCRIPTION

    "gradient" creates a gradient object from a map object.

USAGE

    gradient name, map [, minimum [, maximum [, selection [, buffer [, state
        [, carve [, source_state [, quiet ]]]]]]]]

ARGUMENTS

    map = the name of the map object to use.

    minimum, maximum = minimum and maximum levels (default: full map range)

    selection = an atom selection about which to display the mesh with
        an additional "buffer" (if provided).

SEE ALSO

    load, isomesh

api: pymol.creating.gradient


group

DESCRIPTION

    "group" creates or updates a group object: a container for
    organizing objects into a hierarchy.
    
USAGE

    group name [, members [, action ]]

ARGUMENTS

    name = string: name of the group

    members = string: space-separated list of objects to include in
              the group

    action = add, remove, open, close, toggle, auto, ungroup, empty,
             purge, excise

EXAMPLE

    group kinases, 1oky 1pkg 1t46 1uwh 1z5m
    group kinases, open
    group kinases, close

NOTES

    Group objects can typically be used as arguments to commands.  In
    such cases, the command should be applied to all members of the
    group.  If the group is used as a selection, then all atoms in all
    objects in the group should be included in the selection.

    When a group objects is open, objects can be added or removed from
    the group by right-clicking and dragging in the control panel.

SEE ALSO

    ungroup, order, "group_auto_mode" setting

api: pymol.creating.group


h_add

DESCRIPTION

    "h_add" adds hydrogens onto a molecule based on current valences.

USAGE

    h_add [ selection [, state ]]

ARGUMENTS

    selection = string {default: (all)}

    state = int {default: 0 (all states)}

NOTES

    Because PDB files do not normally contain bond valences for
    ligands and other nonstandard components, it may be necessary to
    manually correct ligand conformations before adding hydrogens.

SEE ALSO

    h_fill

api: pymol.editing.h_add


h_fill

DESCRIPTION

    "h_fill" removes and replaces hydrogens on the atom or bond picked
    for editing.

USAGE

    h_fill

NOTES

    This is useful for fixing hydrogens after changing bond valences.

PYMOL API

    cmd.h_fill()

SEE ALSO

    edit, cycle_valence, h_add

api: pymol.editing.h_fill


h_fix

DESCRIPTION

    "h_fix" is an unsupported command that may have something to do
    with repositioning hydrogen atoms.

api: pymol.editing.h_fix


help

DESCRIPTION

    "help" prints out the online help for a given command.

USAGE

    help command

api: pymol.helping.help


help_setting

DESCRIPTION

    Print documentation for a setting.

USAGE

    help_setting name

api: pymol.helping.help_setting


hide

DESCRIPTION

    "hide" turns off atom and bond representations.


USAGE

    hide [ representation [, selection ]]

ARGUMENTS

    representation = lines, spheres, mesh, ribbon, cartoon,
       sticks, dots, surface, labels, extent, nonbonded, nb_spheres,
       slice, extent, slice, dashes, angles, dihedrals, cgo, cell, callback, 
       or everything

    selection = string: a selection-expression or name-pattern

EXAMPLES

    hide lines, all
    hide ribbon

PYMOL API

    cmd.hide(string representation, string selection)

SEE ALSO

    show, enable, disable

api: pymol.viewing.hide


id_atom

DESCRIPTION

    "id_atom" returns the original source id of a single atom, or
    raises and exception if the atom does not exist or if the selection
    corresponds to multiple atoms.

PYMOL API

    list = cmd.id_atom(string selection)

api: pymol.querying.id_atom


identify

DESCRIPTION

    "identify" returns a list of atom IDs corresponding to the ID code
    of atoms in the selection.

PYMOL API

    list = cmd.identify(string selection="(all)",int mode=0)

NOTES

    mode 0: only return a list of identifiers (default)
    mode 1: return a list of tuples of the object name and the identifier

api: pymol.querying.identify


index

DESCRIPTION

    "index" returns a list of tuples corresponding to the
    object name and index of the atoms in the selection.

PYMOL API

    list = cmd.index(string selection="(all)")

NOTE

  Atom indices are fragile and will change as atoms are added
  or deleted.  Whenever possible, use integral atom identifiers
  instead of indices.

api: pymol.querying.index


indicate

DESCRIPTION

    "indicate" shows a visual representation of an atom selection.

USAGE

    indicate (selection)

PYMOL API

    cmd.count(string selection)

api: pymol.selecting.indicate


intra_fit

DESCRIPTION

        "intra_fit" fits all states of an object to an atom selection
        in the specified state.  It returns the rms values to python
        as an array.

USAGE 

        intra_fit selection [, state]

ARGUMENTS

        selection = string: atoms to fit

        state = integer: target state

PYMOL API

        cmd.intra_fit( string selection, int state )

EXAMPLES

        intra_fit ( name CA )

PYTHON EXAMPLE

        from pymol import cmd
        rms = cmd.intra_fit("(name CA)",1)

SEE ALSO

        fit, rms, rms_cur, intra_rms, intra_rms_cur, pair_fit

api: pymol.fitting.intra_fit


intra_rms

DESCRIPTION

        "intra_rms" calculates rms fit values for all states of an object
        over an atom selection relative to the indicated state.
        Coordinates are left unchanged.  The rms values are returned as a
        python array.

EXAMPLE

        from pymol import cmd
        rms = cmd.intra_rms("(name CA)",1)
        print rms

PYMOL API

        cmd.intra_rms(string selection, int state)

SEE ALSO

        fit, rms, rms_cur, intra_fit, intra_rms_cur, pair_fit

api: pymol.fitting.intra_rms


intra_rms_cur

DESCRIPTION

        "intra_rms_cur" calculates rms values for all states of an object
        over an atom selection relative to the indicated state without
        performing any fitting.  The rms values are returned
        as a python array.

PYMOL API

        cmd.intra_rms_cur( string selection, int state)

PYTHON EXAMPLE

        from pymol import cmd
        rms = cmd.intra_rms_cur("(name CA)",1)

SEE ALSO

        fit, rms, rms_cur, intra_fit, intra_rms, pair_fit

api: pymol.fitting.intra_rms_cur


invert

DESCRIPTION

    "invert" inverts the stereo-chemistry of atom (pk1), holding attached atoms
    (pk2) and (pk3) immobile.

USAGE

    invert 

NOTES

    The invert function is usually bound to CTRL-E in Editing Mode.

PYMOL API

    cmd.invert( )

api: pymol.editing.invert


isodot

DESCRIPTION

    "isodot" creates a dot isosurface object from a map object.

USAGE

    isodot name, map [, level [, selection [, buffer [, state
        [, carve [, source_state [, quiet ]]]]]]]

ARGUMENTS

    map = the name of the map object to use.

    level = the contour level.

    selection = an atom selection about which to display the mesh with
        an additional "buffer" (if provided).

NOTES

    If the dot isosurface object already exists, then the new dots will
    be appended onto the object as a new state.

SEE ALSO

    load, isomesh

api: pymol.creating.isodot


isolevel

DESCRIPTION

    "isolevel" changes the contour level of a isodot, isosurface, or isomesh object.

USAGE

    isolevel name, level, state

api: pymol.creating.isolevel


isomesh

DESCRIPTION

    "isomesh" creates a mesh isosurface object from a map object.

USAGE

    isomesh name, map, level [, selection [, buffer [, state [, carve ]]]]

ARGUMENTS

    name = the name for the new mesh isosurface object.

    map = the name of the map object to use for computing the mesh.

    level = the contour level.

    selection = an atom selection about which to display the mesh with
        an additional "buffer" (if provided).

    state = the state into which the object should be loaded (default=1)
        (set state=0 to append new mesh as a new state)

    carve = a radius about each atom in the selection for which to
        include density. If "carve" is not provided, then the whole
        brick is displayed.

NOTES

    If the mesh object already exists, then the new mesh will be
    appended onto the object as a new state (unless you indicate a state).

    state > 0: specific state
    state = 0: all states
    state = -1: current state
    
    source_state > 0: specific state
    source_state = 0: include all states starting with 0
    source_state = -1: current state
    source_state = -2: last state in map

SEE ALSO

    isodot, load

api: pymol.creating.isomesh


isosurface

DESCRIPTION

    "isosurface" creates a new surface object from a map object.

USAGE

    isosurface name, map, level [, selection [, buffer [, state [, carve ]]]]

ARGUMENTS

    name = the name for the new mesh isosurface object.

    map = the name of the map object to use for computing the mesh.

    level = the contour level.

    selection = an atom selection about which to display the mesh with
        an additional "buffer" (if provided).

    state = the state into which the object should be loaded (default=1)
        (set state=0 to append new surface as a new state)

    carve = a radius about each atom in the selection for which to
        include density. If "carve= not provided, then the whole
        brick is displayed.

NOTES

    If the surface object already exists, then the new surface will be
    appended onto the object as a new state (unless you indicate a state).

SEE ALSO

    isodot, isomesh, load

api: pymol.creating.isosurface


iterate

DESCRIPTION

    "iterate" iterates over an expression within a temporary namespace
    for each atom.

USAGE

    iterate selection, expression

EXAMPLES

    stored.net_charge = 0
    iterate all, stored.net_charge = stored.net_charge + partial_charge
    print stored.net_charge
    
    stored.names = []
    iterate all, stored.names.append(name)
    print stored.names
    
NOTES

    Unlike with the "alter" command, atomic properties cannot be
    altered.  For this reason, "iterate" is more efficient than
    "alter".

SEE ALSO

    iterate_state, alter, alter_state

api: pymol.editing.iterate


iterate_state

DESCRIPTION

    "iterate_state" is to "alter_state" as "iterate" is to "alter"

USAGE

    iterate_state state, selection, expression

EXAMPLES

    stored.sum_x = 0.0
    iterate_state 1, all, stored.sum_x = stored.sum_x + x
    print stored.sum_x
    
SEE ALSO

    iterate, alter, alter_state

api: pymol.editing.iterate_state


join_states

DESCRIPTION

    The reverse of split_states. Create a multi-state object from a
    selection which spans multiple objects.

ARGUMENTS

    name = string: name of object to create or modify

    selection = string: atoms to include in the new object

    mode = int: how to match states {default: 2}
      0: Create discrete object, input objects can be (totally) different
      1: Assume identical topology (same number of atoms and matching atom
         identifiers) in all input objects
      2: Assume matching atom identifiers in all input objects, but also
         check for missing atoms and only include atoms that are present
         in all input objects
      3: match atoms by sequence alignment, slowest but most robust option

EXAMPLE

    fragment ala
    fragment his
    join_states multi, (ala|his), mode=0

api: pymol.creating.join_states


label

DESCRIPTION

    "label" labels one or more atoms in a selection by evaluating an
    Python expression referencing properties for each atom.

USAGE

    label [ selection [, expression ]]

ARGUMENTS

    selection = string: a selection-expression

    expression = string: a Python expression that can be converted to a string
    
EXAMPLES

    label chain A, chain
    label name CA,"%s-%s" % (resn,resi)
    label resi 200,"%1.3f" % partial_charge

NOTES

    The symbols defined in the label name space for each atom are:

        name, resi, resn, resv, chain, segi, model, alt, q, b, type,
        index, rank, ID, ss, vdw, elec_radius, label, elem, geom,
        flags, color, cartoon, valence, formal_charge, partial_charge,
        numeric_type, text_type, stereo

    All strings in the expression must be explicitly quoted.

    This operation typically takes several seconds per thousand atoms
    labelled.

    To clear labels, simply omit the expression or set it to ''.

api: pymol.viewing.label


load

DESCRIPTION

    "load" can by used to read molecules, crystallographic maps and
    other volumetric data, PyMOL sessions, and some other types of
    content.

USAGE

    load filename [, object [, state [, format [, finish [, discrete [, quiet
            [, multiplex [, zoom [, partial [, mimic [, object_props
            [, atom_props ]]]]]]]]]]]]

ARGUMENTS

    filename = string: file path or URL

    object = string: name of the object {default: filename prefix}

    state = integer: number of the state into which
    the content should be loaded, or 0 for append {default:0}

    format = pdb, ccp4, etc. {default: use file extension}): format of
    data file    

    partial = for session files, the partial flag loads the session while
    preserving what is currently loaded in PyMOL.  If it is set to 2,
    then the view that is in the session gets set to the current view

    object_props = argument specifies whether properties should be loaded
    into PyMOL.  If it is a space-delimited list, then only these properties
    will get loaded. If it is a '*', then all properties get loaded.
    If an empty string, then no properties get loaded. {default: use
    load_object_props_default setting}
    
    atom_props = argument specifies whether atom properties should
    be loaded into PyMOL.  If it is a space-delimited list, then only these
    properties will get loaded. If it is a '*', then all properties get loaded.
    If an empty string, then no properties get loaded. {default: use
    load_atom_props_default setting}

EXAMPLES

    load 1dn2.pdb

    load file001.pdb, ligand

    load http://delsci.com/sample.pdb
    
    load file002.mae, ligand, object_props=*

NOTES

    The file extension is used to determine the format unless the
    format is provided explicitly.

    If an object name is specified, then the file is loaded into that
    object.  Otherwise, an object is created with the same name as the
    file prefix.

    If a state value is not specified, then the content is appended
    after the last existing state (if any).

    Supported molecular file formats include: pdb, mol, mol2, sdf,
    xyz, and others.

    Supported map formats include: xplor, ccp4, phi, mtz, and others.

    All supported file formats are covered in the reference
    documentation under File Formats.

PYMOL API

    cmd.load(string filename, string object-name, integer state,
             string format, int finish, int discrete, int quiet,
             int multiplex, int zoom, int partial, string object_props,
             string atom_props)
    
SEE ALSO

    save, load_traj, fetch

api: pymol.importing.load


load_embedded

DESCRIPTION

    "load_embedded" loads content previously defined in the current
    PyMOL command script using the "embed" command.

USAGE

    load_embedded [ key [, name [, state [, finish [, discrete [, quiet ]]]]]]        

EXAMPLE

    embed wats, pdb
    HETATM    1  O   WAT     1       2.573  -1.034  -1.721
    HETATM    2  H1  WAT     1       2.493  -1.949  -1.992
    HETATM    3  H2  WAT     1       2.160  -0.537  -2.427
    HETATM    4  O   WAT     2       0.705   0.744   0.160
    HETATM    5  H1  WAT     2      -0.071   0.264   0.450
    HETATM    6  H2  WAT     2       1.356   0.064  -0.014
    embed end

    load_embedded wats

NOTES

    This approach only works with text data files.

api: pymol.importing.load_embedded


load_mtz

DESCRIPTION

    Load a MTZ file as two map objects (fofc, 2fofc) or if amplitudes and
    phases column names are given, as one map object.

USAGE

    load_mtz filename [, prefix [, amplitudes, phases [, weights
        [, reso_low [, reso_high ]]]]]

ARGUMENTS

    filename = str: filename

    prefix = str: object name or prefix {default: filename without extension}

    amplitudes = str: amplitudes column name, guess if blank {default: }

    phases = str: phases column name, required if amplitudes are given {default: }

    weights = str: weights column name, optional {default: None}

    reso_low = float: minimum resolution {default: 0, read from file}

    reso_high = float: maximum resolution {default: 0, read from file}

api: pymol.importing.load_mtz


load_png

DESCRIPTION

    "load_png" loads and displays a PNG file from disk.

USAGE

    load_png filename

NOTES

    If the displayed image is too big for the window, it will be
    reduced 2-fold repeatedly until it fits.

api: pymol.viewing.load_png


load_traj

DESCRIPTION

    "load_traj" reads trajectory files.

    Most of the trajectory formats listed here are supported:
    http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/

USAGE

    load_traj filename [,object [,state [,format [,interval [,average ]
                             [,start [,stop [,max [,selection [,image [,shift
                             ]]]]]]]]]

PYMOL API

    cmd.load_traj(filename,object='',state=0,format='',interval=1,
                  average=1,start=1,stop=-1,max=-1,selection='all',image=1,
                  shift="[0.0,0.0,0.0]")

NOTES

    You must first load a corresponding topology file before attempting
    to load a trajectory file.

    PyMOL does not know how to wrap the truncated octahedron used by Amber
    You will need to use the "ptraj" program first to do this.

    The average option is not a running average.  To perform this type of
    average, use the "smooth" command after loading the trajectory file.

SEE ALSO

    load

api: pymol.importing.load_traj


loadall

DESCRIPTION

    Load all files matching given globbing pattern

USAGE

    loadall pattern [, group ]

EXAMPLE

    loadall *.pdb

api: pymol.importing.loadall


log

DESCRIPTION

    "log" writes a command to the log file (if one is open).

    `text` and/or `alt_text` must include the terminating line feed.

ARGUMENTS

    text = str: PyMOL command (optional if alt_text is given)
    alt_text = str: Python expression (optional)

SEE ALSO

    log_open, log_close

api: pymol.commanding.log


log_close

DESCRIPTION

    "log_close" closes the current log file (if one is open).

USAGE

    log_close

SEE ALSO

    log, log_open

api: pymol.commanding.log_close


log_open

DESCRIPTION

    "log_open" opens a log file for writing.

USAGE

    log_open filename

SEE ALSO

    log, log_close

api: pymol.commanding.log_open


ls

DESCRIPTION

    List contents of the current working directory.

USAGE

    ls [pattern]
    dir [pattern]

EXAMPLES

    ls
    ls *.pml

SEE ALSO

    cd, pwd, system

api: pymol.externing.ls


madd

DESCRIPTION

    "madd" extends the existing movie specification using the same
    syntax as mset.

SEE ALSO

    mset, mdo, mplay, mclear

api: pymol.moving.madd


map_double

DESCRIPTION

    "map_double" resamples a map at twice the current resolution.

NOTES

     The amount of memory required to store the map will increase
     eight-fold.

USAGE

    map_double map_name, state

api: pymol.editing.map_double


map_halve

DESCRIPTION

    "map_halve" resamples a map at half the current resolution.  

USAGE

    map_halve map_name, state
    
NOTES

    The amount of memory required to store the map will decrease
    eight-fold.

SEE ALSO

    map_double

api: pymol.editing.map_halve


map_new

DESCRIPTION

    "map_new" creates a map object using one of the built-in map
    generation routines.  This command not yet fully supported.

USAGE

    map_new name [, type [, grid [, selection [, buffer [, box [, state ]]]]]]

ARGUMENTS

    name = string: name of the map object to create or modify
	
    type = vdw, gaussian, gaussian_max, coulomb, coulomb_neutral, coulomb_local

    grid = float: grid spacing

    selection = string: atoms about which to generate the map

    buffer = float: cutoff 
    
    state > 0: use the indicated state
    
    state = 0: use all states independently with independent extents
    
    state = -1: use current global state
    
    state = -2: use effective object state(s)
    
    state = -3: use all states in one map
    
    state = -4: use all states independent states by with a unified extent

NOTES

    This command can be used to create low-resolution surfaces of
    protein structures.

api: pymol.creating.map_new


map_set

DESCRIPTION

    "map_set" provides a number of common operations on and between maps.

USAGE

    map_set name, operator, operands, target_state, source_state

    operator may be "minimum, maximum, average, sum, or difference"

EXAMPLES

    map my_sum, add, map1 map2 map3
    map my_avg, average, map1 map2 map3
    
NOTES

    source_state = 0 means all states
    target_state = -1 means current state
    
    experimental
    
SEE ALSO

    map_new

api: pymol.editing.map_set


map_set_border

DESCRIPTION

    "map_set_border" is a function (reqd by PDA) which allows you to set the
    level on the edge points of a map

USAGE

    map_set_border name, level

NOTES

    unsupported.
    
SEE ALSO

    load

api: pymol.editing.map_set_border


map_trim

DESCRIPTION

    "map_trim" is an unsupported command that may have something to do with
    reducing the extent of a map to cover just a single selection of atoms.

api: pymol.editing.map_trim


mappend

DESCRIPTION

    "mappend" associates additional command line operations with a
    particular movie frame.  These "generalized movie commands" will
    be executed every time the numbered frame is played.
    
USAGE

    mappend frame: command

ARGUMENTS

    frame = integer: the frame to modify

    command = literal command-line text
    
EXAMPLE

    mappend 1: hide everything; show sticks
    mappend 60: hide sticks; show spheres
    mappend 120: hide spheres; show surface
    
NOTES

    The "mset" command must first be used to define the movie before
    "mdo" statements will have any effect.  Redefinition of the movie
    clears any existing movie commands specified with mdo or mappend.

SEE ALSO

    mset, madd, mdo, mplay, mstop

api: pymol.moving.mappend


mask

DESCRIPTION

    "mask" makes it impossible to select the indicated atoms using the
    mouse.  This is useful when you are working with one molecule in
    front of another and wish to avoid accidentally selecting atoms in
    the background.

USAGE

    mask (selection)

PYMOL API

    cmd.mask( string selection="(all)" )

SEE ALSO

    unmask, protect, deprotect, mouse

api: pymol.controlling.mask


matrix_copy

DESCRIPTION
        
    "matrix_copy" copies a transformation matrix from one object to
    another.

USAGE

    matrix_copy source_name, target_name

NOTES

    This command is often used after a protein structure alignment to
    bring other related objects into the same frame of reference.

SEE ALSO

    matrix_reset, align, fit, pair_fit

api: pymol.editing.matrix_copy


matrix_reset

DESCRIPTION
        
    "matrix_reset" resets the transformation for an object.

USAGE

    matrix_reset name [, state [, mode ]]

ARGUMENTS

    name = str: object name

    state = int: object state {default: 1}

    mode = int: {defualt: -1 = matrix_mode or 0}
      0: transformation was applied to coordinates
      1: reset TTT matrix (movie transformation)
      2: reset state matrix

SEE ALSO

    matrix_copy, align, super, fit, pair_fit

api: pymol.editing.matrix_reset


mclear

DESCRIPTION

    "mclear" clears the movie frame image cache.

USAGE

    mclear

PYMOL API

    cmd.mclear()

api: pymol.moving.mclear


mcopy

DESCRIPTION

    "mcopy" copies key frames and movie commands

    Usage like "mmove".

SEE ALSO

    mmove, mdelete, minsert

api: pymol.moving.mcopy


mdelete

DESCRIPTION

    "mdelete" removes frames from camera view and object motions.

ARGUMENTS

    count = int: number of frames to delete, or -1 to delete all the way
    to the end {default: -1}

    frame = int: first frame to delete, or 0 for current frame {default: 0}

EXAMPLE

    # delete frames 81 to 90
    mdelete 10, 81

SEE ALSO

    minsert, mmove

api: pymol.moving.mdelete


mdo

DESCRIPTION

    "mdo" defines (or redefines) the command-line operations
    associated with a particular movie frame.  These "generalized
    movie commands" will be executed every time the numbered frame is
    played.

USAGE

    mdo frame: command

PYMOL API

    cmd.mdo( int frame, string command )

EXAMPLE

    // Creates a single frame movie involving a rotation about X and Y

    load test.pdb
    mset 1
    mdo 1, turn x,5; turn y,5;
    mplay

NOTES

 These commands are usually created
    by a PyMOL utility program (such as movie.rock).  Command can
    actually contain several commands separated by semicolons ';'
    
    The "mset" command must first be used to define the movie before
    "mdo" statements will have any effect.  Redefinition of the movie
    clears any existing mdo statements.

SEE ALSO

    mset, mplay, mstop

api: pymol.moving.mdo


mdump

DESCRIPTION

    "mdump" dumps the current set of movie commands as text output.

USAGE

    mdump

SEE ALSO

    mplay, mset, mdo, mclear, mmatrix

api: pymol.moving.mdump


mem

DESCRIPTION

    "mem" Dumps current memory state to standard output. This is a
    debugging feature, not an official part of the API.

api: pymol.experimenting.mem


meter_reset

DESCRIPTION

    "meter_reset" resets the frames per secound counter.

USAGE

    meter_reset

api: pymol.viewing.meter_reset


middle

DESCRIPTION

    "middle" goes to the middle of the movie.

USAGE

    middle

PYMOL API

    cmd.middle()

api: pymol.moving.middle


minsert

DESCRIPTION

    "minsert" adds frames into camera view and object motions.

ARGUMENTS

    count = int: number of frames to insert

    frame = int: insert before "frame" if frame > 0, otherwise insert before
    the current frame {default: 0}

SEE ALSO

    mdelete, mmove, madd

api: pymol.moving.minsert


mmatrix

DESCRIPTION

    "mmatrix" sets up a matrix to be used for the first frame of the movie.

USAGE

    mmatrix action

ARGUMENTS

    action = clear, store, or recall

NOTES

    This command ensures that the movie always starts from the same
    camera view.

    "mmatrix" should not be used when controlling the camera using
    "mview".
    
PYMOL API

    cmd.mmatrix( string action )

EXAMPLES

    mmatrix store

api: pymol.moving.mmatrix


mmove

DESCRIPTION

    "mmove" moves key frames and movie commands

ARGUMENTS

    target = int: frame to move to

    source = int: frame to move from, 0 for current frame {default: 0}

    count = int: number of frames to move

SEE ALSO

    mcopy, mdelete, minsert

api: pymol.moving.mmove


morph

DESCRIPTION

    Creates an interpolated trajectory between two or multiple conformations.
    If the two input objects are not the same, match them based on sequence
    alignment.

    This command supports two methods: rigimol and linear. RigiMOL is an
    incentive feature and only available to official PyMOL sponsors. Linear
    morphing is quick and robust but likely to produce distorted intermediates.

ARGUMENTS

    name = string: name of object to create

    sele1 = string: atom selection of first conformation

    sele2 = string: atom selection of second conformation {default: <sele1>}

    state1 = int: sele1 state {default: 1}. If state1=0 and sele1 has N
    states, create N morphings between all consecutive states and back from
    state N to 1 (so the morph will have N*steps states). If state2=0, create
    N-1 morphings and stop at last state.

    state2 = int: sele2 state {default: 2 if sele1=sele2, else 1}

    refinement = int: number of sculpting refinement cycles to clean
    distorted intermediates {default: 3}

    steps = int: number of states for sele2 object {default: 30}

    method = string: rigimol or linear {default: rigimol}

EXAMPLE

    fetch 1akeA 4akeA, async=0
    align 1akeA, 4akeA
    morph mout, 1akeA, 4akeA

api: pymol.morphing.morph


mouse

DESCRIPTION

    "mouse" cycles through the mouse modes defined in the current
    mouse configuration ring.

USAGE

    mouse

api: pymol.controlling.mouse


move

DESCRIPTION

    "move" translates the camera about one of the three primary axes.

USAGE

    move axis, distance

EXAMPLES

    move x, 3
    move y, -1

PYMOL API

    cmd.move(string axis, float distance)

SEE ALSO

    turn, rotate, translate, zoom, center, clip

api: pymol.viewing.move


movie.load

UNDOCUMENTED

api: pymol.movie.load


movie.nutate

UNDOCUMENTED

api: pymol.movie.nutate


movie.pause

UNDOCUMENTED

api: pymol.movie.pause


movie.produce

DESCRIPTION

    Export a movie to an MPEG file.

    Requires FREEMOL.

ARGUMENTS

    filename = str: filename of MPEG file to produce

    mode = draw or ray: {default: check "ray_trace_frames" setting}

    first = int: first frame to export {default: 1}

    last = int: last frame to export {default: last frame of movie}

    preserve = 0 or 1: don't delete temporary files {default: 0}

    quality = 0-100: encoding quality {default: 90 (movie_quality setting)}

api: pymol.movie.produce


movie.rock

UNDOCUMENTED

api: pymol.movie.rock


movie.roll

UNDOCUMENTED

api: pymol.movie.roll


movie.screw

UNDOCUMENTED

api: pymol.movie.screw


movie.sweep

UNDOCUMENTED

api: pymol.movie.sweep


movie.tdroll

AUTHOR

    Byron DeLaBarre

USAGE

    movie.tdroll(rangx,rangey,rangez,skip=1,mset=0)
    
    rangex/y/z = rotation range on respective axis
    enter 0 for no rotation.

    skip is angle increment in each frame
    
    Use skip to reduce final movie size or to speed up rotation.
    
EXAMPLE

    movie.tdroll 360,360,360,5

api: pymol.movie.tdroll


movie.zoom

UNDOCUMENTED

api: pymol.movie.zoom


mplay

DESCRIPTION

    "mplay" starts the movie.

USAGE

    mplay

PYMOL API

    cmd.mplay()

SEE ALSO

    mstop, mset, mdo, mclear, mmatrix

api: pymol.moving.mplay


mpng

DESCRIPTION

    "mpng" writes movie frames as a series of numbered png files.

USAGE

    mpng prefix [, first [, last [, preserve [, modal [, mode [, quiet
        [, width [, height ]]]]]]]]

ARGUMENTS

    prefix = string: filename prefix for saved images -- output files
    will be numbered and end in ".png"

    first = integer: starting frame {default: 0 (first frame)}

    last = integer: last frame {default: 0 (last frame)}

    preserve = 0/1: Only write non-existing files {default: 0}

    modal = integer: will frames be rendered with a modal draw loop

    mode = int: 2=ray, 1=draw, 0=normal {default: -1, check
    ray_trace_frames or draw_frames}

    width = int: width in pixels {default: current viewport}

    height = int: height in pixels {default: current viewport}
    
NOTES

    If the "ray_trace_frames" variable is non-zero, then the frames
    will be ray-traced.  Note that this can take many hours for a long
    movie with complex content displayed.

    Also, be sure to avoid setting "cache_frames" when rendering a
    long movie to avoid running out of memory.
    
    Arguments "first" and "last" can be used to specify an inclusive
    interval over which to render frames.  Thus, you can write a smart
    Python program that will automatically distribute rendering over a
    cluster of workstations.  If these options are left at zero, then
    the entire movie will be rendered.

PYMOL API

    cmd.mpng(string prefix, int first, int last)

SEE ALSO

    png, save

api: pymol.moving.mpng


mse2met

DESCRIPTION

    Mutate selenomethionine to methionine

api: pymol.editing.mse2met


mset

DESCRIPTION

    "mset" sets up a relationship between molecular states and movie
    frames.  This makes it possible to control which states are shown
    in which frame.

USAGE

    mset specification [ ,frame ]

PYMOL API

    cmd.mset( string specification [, int frame] )

EXAMPLES

    # simplest case, one state -> one frame

    mset 1

    # ten frames, all corresponding to state 1
    
    mset 1 x10     

    # the first thirty frames are state 1
    # the next 15 frames pass through states 1-15
    # the next 30 frames are of state 15
    # the next 15 frames iterate back to state 1

    mset 1 x30 1 -15 15 x30 15 -1

SEE ALSO

    madd, mdo, mplay, mclear

api: pymol.moving.mset


mstop

DESCRIPTION

    "mstop" stops playing of the movie.

USAGE

    mstop

SEE ALSO

    mplay, mset, mdo, mclear, mmatrix

api: pymol.moving.mstop


mtoggle

DESCRIPTION

    "mtoggle" toggles playing of the movie.

api: pymol.moving.mtoggle


multifilesave

DESCRIPTION

    For a selection that spans multiple molecular objects and/or states,
    save each object and/or state to a separate file. Takes a filename
    argument with placeholders:

    {name}  : object name
    {state} : state number
    {title} : state title
    {num}   : file number
    {}      : object name (first) or state (second)

EXAMPLES

    multifilesave /tmp/{name}.pdb
    multifilesave /tmp/{name}-{state}.cif, state=0
    multifilesave /tmp/{}-{}.cif, state=0
    multifilesave /tmp/{}-{title}.sdf, state=0

api: pymol.exporting.multifilesave


multisave

DESCRIPTION

    "multisave" will save a multi-entry PDB file.

    Every object in the given selection (pattern) will have a HEADER and a
    CRYST (if symmetry is defined) record, and is terminated with END.
    Loading such a multi-entry PDB file into PyMOL will load each entry
    as a separate object.

    This behavior is different to the "save" command, where a multi-object
    selection is written "flat" to a PDB file, without HEADER or CRYST
    records.

ARGUMENTS

    filename = string: file path to be written

    pattern = str: atom selection (before 1.8.4: object name pattern)

    state = int: object state (-1=current, 0=all) {default: -1}

    append = 0/1: append to existing file {default: 0}

    format = str: file format {default: guess from extension, or 'pdb'}

api: pymol.exporting.multisave


mview

DESCRIPTION

    "mview" stores camera and object matrices for use in movie
    interpolation.

USAGE

    mview [action [, first [, last [, power [, bias [, simple
       [, linear [, object [, wrap [, hand [, window [, cycles [,scene
       [, cut [, quiet ]]]]]]]]]]]]]]]

ARGUMENTS

    action = str: one of store, clear, reset, purge, interpolate,
    uninterpolate, reinterpolate, toggle, toggle_interp, smooth
    {default: store}

    first = int: frame number or 0 for current frame {default: 0}

    power = float: slow down animation at keyframe (0.0) or not (1.0)
    {default: 0.0}

    object = str: name of object for object keyframes, or empty for
    global (camera) keyframes {default: }

    scene = str: name of scene to store scene with key frame {default: }

    cut = float 0.0-1.0: scene switch moment (0.0: beginning of transition,
    1.0: end of transition) {default: 0.5}

    auto = -1/0/1: if freeze=0, then auto reinterpolate after store, clear,
    or toggle {default: -1 = use movie_auto_interpolate}

    state = int: if > 0, then store object state {default: 0}

    freeze = 0/1: never auto reinterpolate {default: 0}

SEE ALSO

    mplay, mset, mdo, mclear, mmatrix

api: pymol.moving.mview


order

DESCRIPTION

    "order" changes the ordering of names in the control panel.

USAGE

    order names, sort, location

ARGUMENTS

    names = string: a space-separated list of names

    sort = yes or no {default: no}

    location = top, current, or bottom {default: current}

EXAMPLES

    order 1dn2 1fgh 1rnd       # sets the order of these three objects
    order *,yes                # sorts all names
    order 1dn2_*, yes          # sorts all names beginning with 1dn2_
    order 1frg, location=top   # puts 1frg at the top of the list

PYMOL API

    cmd.order(string names, string sort, string location)

NOTES

    "order" can also be used to reorder objects within a group.
    
SEE ALSO

    set_name, group

api: pymol.controlling.order


orient

DESCRIPTION

    "orient" aligns the principal components of the atoms in the
    selection with the XYZ axes.  

USAGE

    orient [ selection [, state [, animate ]]]

ARGUMENTS

    selection = a selection-expression or name-pattern {default: (all)}

    state = 0: use all coordinate states {default}
    
    state = -1: uses only coordinates for the current state
    
    state > 0: uses coordinates for a specific state

EXAMPLES

    orient organic

NOTES

    The function is similar to the orient command in X-PLOR.

PYMOL API

    cmd.orient(string object-or-selection, int state, float animate)

SEE ALSO

    zoom, origin, reset

api: pymol.viewing.orient


origin

DESCRIPTION

    "origin" sets the center of rotation about a selection.  If an
    object name is specified, it can be used to set the center of
    rotation for the object (for use in animation and editing).

USAGE

    origin [ selection [, object [,position, [, state ]]]]

ARGUMENTS

    selection = string: selection-expression or name-list {default: (all)}
    
    state = 0 (default) use all coordinate states
    
    state = -1 use only coordinates for the current state
    
    state > 0  use coordinates for a specific state

EXAMPLES

    origin chain A
    
    origin position=[1.0,2.0,3.0]

PYMOL API

    cmd.origin(string object-or-selection)

SEE ALSO

    zoom, orient, reset

api: pymol.viewing.origin


overlap

DESCRIPTION

    "overlap" is an unsupported command that sums up
    [(VDWi + VDWj) - distance_ij]/2 between pairs of
    selected atoms.

PYMOL API

    cmd.overlap(string selection1, string selection2 [, int state1=1, int state2=1, float adjust=0.0])

NOTES

    It does not compute the volume overlap,
    selections with more atoms will have a larger
    sum.

api: pymol.querying.overlap


pair_fit

DESCRIPTION

	"pair_fit" fits matched sets of atom pairs between two objects.

USAGE

	pair_fit selection, selection, [ selection, selection [ ... ]]

EXAMPLES

	# superimpose protA residues 10-25 and 33-46 to protB residues 22-37 and 41-54:
	
	pair_fit protA/10-25+33-46/CA, protB/22-37+41-54/CA

	# superimpose ligA atoms C1, C2, and C4 to ligB atoms C8, C4, and C10, respectively:
	
	pair_fit ligA////C1, ligB////C8, ligA////C2, ligB////C4, ligA////C3, ligB////C10
	
NOTES

	So long as the atoms are stored in PyMOL with the same order
	internally, you can provide just two selections.  Otherwise, you
	may need to specify each pair of atoms separately, two by two, as
	additional arguments to pair_fit.
	
	Script files are usually recommended when using this command.

SEE ALSO

	fit, rms, rms_cur, intra_fit, intra_rms, intra_rms_cur

api: pymol.fitting.pair_fit


phi_psi

DESCRIPTION

    "phi_psi" return the phi and psi angles for a protein atom
    selection.
    
USAGE

api: pymol.querying.phi_psi


pip

DESCRIPTION

    Experimental and limited pip support for installing additional Python
    packages into PyMOL's bundled Python distribution. Type "pip help" for
    more information.

EXAMPLE

    pip install tkintertable

api: pymol.externing.pip


png

DESCRIPTION

    "png" saves a PNG format image file of the current display.

USAGE

    png filename [, width [, height [, dpi [, ray]]]]

ARGUMENTS

    filename = string: file path to be written
    
    width = integer or string: width in pixels (without units), inches (in)
    or centimeters (cm). If unit suffix is given, dpi argument is required
    as well. If only one of width or height is given, the aspect ratio of
    the viewport is preserved. {default: 0 (current)}

    height = integer or string: height (see width) {default: 0 (current)}

    dpi = float: dots-per-inch {default -1.0 (unspecified)}

    ray = 0 or 1: should ray be run first {default: 0 (no)}

EXAMPLES

    png image.png
    png image.png, dpi=300
    png image.png, 10cm, dpi=300, ray=1

NOTES

    PNG is the only image format supported by PyMOL.

SEE ALSO

    mpng, save
    
PYMOL API

    cmd.png(string filename, int width, int height, float dpi,
            int ray, int quiet)

api: pymol.exporting.png


pop

DESCRIPTION

    "pop" provides a mechanism of iterating through an atom selection
    atom by atom, where each atom is sequentially assigned to the
    named selection.
    
USAGE

    pop name, source
    
EXAMPLE

    select src, name CA

    python
    while cmd.pop("tmp","src"):
        cmd.zoom("tmp",2, animate=1)
        for a in range(30):
           cmd.refresh()
           time.sleep(0.05)
    python end
    
PYMOL API

    cmd.deselect()

api: pymol.selecting.pop


protect

DESCRIPTION

    "protect" protects a set of atoms from tranformations performed
    using the editing features.  This is most useful when you are
    modifying an internal portion of a chain or cycle and do not wish
    to affect the rest of the molecule.

USAGE

    protect (selection)

PYMOL API

    cmd.protect(string selection)

SEE ALSO

    deprotect, mask, unmask, mouse, editing

api: pymol.editing.protect


pseudoatom

DESCRIPTION

    "pseudoatom" adds a pseudoatom to a molecular object, and will
    creating the molecular object if it does not yet exist.
    
USAGE

    pseudoatom object [, selection [, name [, resn [, resi [, chain
        [, segi [, elem [, vdw [, hetatm [, b [, q [, color [, label
        [, pos [, state [, mode [, quiet ]]]]]]]]]]]]]]]]]

NOTES

    "pseudoatom" can be used for a wide variety of random tasks where
    on must place an atom or a label in 3D space.

api: pymol.creating.pseudoatom


pwd

DESCRIPTION

    Print current working directory.

USAGE

    pwd

SEE ALSO

    cd, ls, system

api: pymol.externing.pwd


python

DESCRIPTION

    "python" delimits a block of literal Python code embedded in a
    PyMOL command script.

EXAMPLE

    python

    for a in range(1,10):
        b = 10 - a
        print a, b

    python end

NOTES

    Literal Python blocks avoid the annoying requirement of having to
    use explicit line continuation markers for multi-line Python
    commands embedded within Python scripts.  
    
SEE ALSO

    abort, embed, skip

api: pymol.helping.python


quit

DESCRIPTION

    "quit" terminates the program. 

USAGE

    quit [code]

ARGUMENTS

    code = int: exit the application with status "code" {default: 0}

PYMOL API

    cmd.quit(int code)

api: pymol.commanding.quit


ramp_new

DESCRIPTION

    "ramp_new" creates a color ramp based on a map potential value or
    based on proximity to a molecular object.
    
USAGE

    ramp_new name, map_name [, range [, color [, state [, selection [,
        beyond [, within [, sigma [, zero ]]]]]]]]

ARGUMENTS

    name = string: name of the ramp object

    map_name = string: name of the map (for potential) or molecular
    object (for proximity)
    
    range = list: values corresponding to slots in the ramp

    color = list: colors corresponding to slots in the ramp

    state = integer: state identifier

    selection = selection: for automatic ranging
    
    beyond = number: with automatic ranging, are we excluding
    values beyond a certain distance from the selection?

    within = number: with automatic ranging, are we only including
    valuess within a certain distance from the selection?

    sigma = number: with automatic ranging, how many standard
    deviations from the mean do we go?

    zero = integer: with automatic ranging, do we force the central
    value to be zero?

EXAMPLES

    ramp_new e_pot_color, e_pot_map, [-10,0,10], [red,white,blue]

NOTES

    Color ramps are extremely powerful but complicated to use.

    In the simplest case, they can be used to color representations
    based on the potential values found in a map object at the
    corresponding positions in space.

    In another simple case, representations can be colored based on
    proximity to a target.  Note that since ramp targets must
    themselves be real objects (not merely selections), the "create"
    command may be needed in order to generate an appropriate target.
    
    In more complicated cases, they can be used to color
    representations on one object based atoms found in another.

    Ramps can operate recursively.  In other words, the output color
    from one ramp can be used as the input color for another.  For
    example, you could color by map potential within a certain
    distance of the target object, beyond which, a uniform color is applied.
    
    
PYMOL API

    def ramp_new(string name, string map_name, list range, list color,
                 int state, string selection, float beyond, float
                 within, float sigma, int zero, int quiet)

SEE ALSO

    ramp_update, load, color, create, slice, gradient

api: pymol.creating.ramp_new


ramp_update

DESCRIPTION

    "ramp_update" updates range and/or color of a color ramp.

USAGE

    ramp_update name [, range [, color ]]

EXAMPLES

    ramp_new    e_pot_color, e_pot_map, [-10,0,10], [red,white,blue]
    ramp_update e_pot_color, range=[-15,0,15]
    ramp_update e_pot_color, color=[green,white,orange]

SEE ALSO

    ramp_new

api: pymol.creating.ramp_update


ray

DESCRIPTION

    "ray" creates a ray-traced image of the current frame. This
    can take some time (up to several minutes, depending on image
    complexity).

USAGE

    ray [width [,height [,antialias [,angle [,shift [,renderer [,quiet
        [,async ]]]]]]]]]

ARGUMENTS

    width = integer {default: 0 (current)}

    height = integer {default: 0 (current)}

    antialias = integer {default: -1 (use antialias setting)}

    angle = float: y-axis rotation for stereo image generation
    {default: 0.0}

    shift = float: x-axis translation for stereo image generation
    {default: 0.0}

    renderer = -1, 0, 1, or 2: respectively, default, built-in,
    pov-ray, or dry-run {default: 0}
    
    async = 0 or 1: should rendering be done in a background thread?
    
EXAMPLES

    ray
    ray 1024,768
    ray renderer=2

NOTES

    Default width and height are taken from the current viewpoint. If
    one is specified but not the other, then the missing value is
    scaled so as to preserve the current aspect ratio.
    
    angle and shift can be used to generate matched stereo pairs

    renderer = 1 uses PovRay.  This is Unix-only and you must have
        "povray" in your path.  It utilizes two two temporary files:
        "tmp_pymol.pov" and "tmp_pymol.png".

    See "help faster" for optimization tips with the builtin renderer.
    See "help povray" for how to use PovRay instead of PyMOL's
    built-in ray-tracing engine.

PYMOL API

    cmd.ray(int width, int height, int antialias, float angle,
            float shift, int renderer, int quiet, int async)
SEE ALSO

    draw, png, save

api: pymol.viewing.ray


rebuild

DESCRIPTION

    "rebuild" forces PyMOL to recreate geometric objects in
    case any of them have gone out of sync.

USAGE

    rebuild [selection [, representation ]]

ARGUMENTS

    selection = string {default: all}

    representation = string: {default: everything}

PYMOL API

    cmd.rebuild(string selection, string representation)

SEE ALSO

    refresh

api: pymol.viewing.rebuild


recolor

DESCRIPTION

    "recolor" forces reapplication of colors to existing objects.
    
USAGE

    recolor [selection [, representation ]]

ARGUMENTS

    selection = string {default: all}

    representation = string {default: everything}
    
NOTES

    This command often needs to be executed after "set_color" has been
    used to redefine one or more existing colors.
    
PYMOL API

    cmd.recolor(string selection = 'all', string representation = 'everything')

SEE ALSO

    color, set_color

api: pymol.viewing.recolor


redo

DESCRIPTION

    "redo" reapplies the conformational change of the object currently
    being edited.

USAGE

    redo

SEE ALSO

    undo, push_undo

api: pymol.editing.redo


reference

UNDOCUMENTED

api: pymol.editing.reference


refresh

DESCRIPTION

    "refresh" causes the scene to be redrawn as soon as the operating
    system allows it to be done.

USAGE

    refresh

PYMOL API

    cmd.refresh()

SEE ALSO

    rebuild

api: pymol.viewing.refresh


refresh_wizard

DESCRIPTION

    "refresh_wizard" is in unsupported internal command.

api: pymol.wizarding.refresh_wizard


reinitialize

DESCRIPTION

    "reinitialize" reinitializes the program by deleting all objects
    and restoring the default program settings.

USAGE

    reinitialize

api: pymol.commanding.reinitialize


remove

DESCRIPTION

    "remove" eleminates the atoms in a selection from their respective
    molecular objects.

USAGE

    remove selection

EXAMPLES

    remove resi 124 

PYMOL API

    cmd.remove( string selection )

SEE ALSO

    delete

api: pymol.editing.remove


remove_picked

DESCRIPTION

    "remove_picked" removes the atom or bond currently picked for
    editing.

USAGE

    remove_picked [ hydrogens ]

NOTES

    This function is usually connected to the
    DELETE key and "CTRL-D".

    By default, attached hydrogens will also be deleted unless
    hydrogen-flag is zero.

PYMOL API

    cmd.remove_picked(integer hydrogens)

SEE ALSO

    attach, replace

api: pymol.editing.remove_picked


rename

DESCRIPTION

    "rename" creates new atom names which are unique within residues.

USAGE

    rename selection [, force ]

PYMOL API

    cmd.rename(string selection, int force )

SEE ALSO

    alter

api: pymol.editing.rename


replace

DESCRIPTION

    "replace" replaces the picked atom with a new atom.

USAGE

    replace element, geometry, valence [, h_fill [, name ]]

NOTES

    Immature functionality. See code for details.

PYMOL API

    cmd.replace(string element, int geometry, int valence, int h_fill,
                string name)

SEE ALSO

    remove, attach, fuse, bond, unbond

api: pymol.editing.replace


replace_wizard

DESCRIPTION

    "replace_wizard" is an unsupported internal command.

api: pymol.wizarding.replace_wizard


reset

DESCRIPTION

    "reset" restores the rotation matrix to identity, sets the origin
    to the center of mass (approx.) and zooms the window and clipping
    planes to cover all objects.  Alternatively, it can reset object
    matrices.

USAGE

    reset [ object ]

PYMOL API

    cmd.reset()

api: pymol.viewing.reset


resume

DESCRIPTION

    "resume" executes a log file and opens it for recording of
    additional commands.

USAGE

    resume filename

SEE ALSO

    log, log_close

api: pymol.commanding.resume


rewind

DESCRIPTION

    "rewind" goes to the beginning of the movie.

USAGE

    rewind

PYMOL API

    cmd.rewind()

api: pymol.moving.rewind


rms

DESCRIPTION

	"rms" computes a RMS fit between two atom selections, but does not
	tranform the models after performing the fit.

USAGE

	rms (selection), (target-selection)

EXAMPLES

	fit ( mutant and name CA ), ( wildtype and name CA )

SEE ALSO

	fit, rms_cur, intra_fit, intra_rms, intra_rms_cur, pair_fit

api: pymol.fitting.rms


rms_cur

DESCRIPTION

	"rms_cur" computes the RMS difference between two atom
	selections without performing any fitting.

USAGE

	rms_cur (selection), (selection)

SEE ALSO

	fit, rms, intra_fit, intra_rms, intra_rms_cur, pair_fit

api: pymol.fitting.rms_cur


rock

DESCRIPTION

    "rock" toggles Y axis rocking.

USAGE

    rock

PYMOL API

    cmd.rock()

api: pymol.viewing.rock


rotate

DESCRIPTION

    "rotate" rotates the atomic coordinates of atoms in a selection
    about an axis.  Alternatively, it modifies the matrix associated
    with a particular object or object state.

USAGE

    rotate axis, angle [, selection [, state [, camera [, object 
        [, origin ]]]]]

ARGUMENTS

    axis = x, y, z, or float vector: axis about which to rotate

    angle = float: degrees of rotation

    selection = string: atoms whose coordinates should be modified {default: all}
    
    state > 0: only the indicated state is modified

    state = 0: all states are modified

    state = -1: only the current state is modified {default}

    camera = 0 or 1: is the axis specific in camera coordinates? {default: 1}

    object = string: object name (only if rotating object matrix) {default: None}

    origin = float vector: origin of rotateion {default: None}
        
EXAMPLES

    rotate x, 45, pept

    rotate [1,1,1], 10, chain A

NOTES

    Behavior differs depending on whether or not the "object"
    parameter is specified.

    If object is None, then the atomic coordinates are modified
    directly, and all representation geometries will need to be
    regenerated to reflect the new atomic coordinates.

    If object is set to an object name, then the selection field is
    ignored and instead of translating the atomic coordinates, the
    object matrix is modified.  This option is only intended for use
    in animations and is not yet fully supported.

PYMOL API

    cmd.rotate(list-or-string axis, float angle, string selection, 
               int state, int camera, string object)

api: pymol.editing.rotate


run

DESCRIPTION

    "run" executes an external Python script in a local name space,
    the main Python namespace, the global PyMOL namespace, or in its
    own namespace (as a module).

USAGE

    run file [, namespace ]

ARGUMENTS

    file = string: a Python program, typically ending in .py or .pym.

    namespace = local, global, module, main, or private {default: global}

NOTES

    Due to an idiosyncracy in Pickle, you can not pickle objects
    directly created at the main level in a script run as "module",
    (because the pickled object becomes dependent on that module).
    Workaround: delegate construction to an imported module.

SEE ALSO

    spawn

api: pymol.parsing.run


save

DESCRIPTION

    "save" writes content to a file.
    
USAGE

    save filename [, selection [, state [, format ]]]

ARGUMENTS

    filename = string: file path to be written

    selection = string: atoms to save {default: (all)}

    state = integer: state to save {default: -1 (current state)}
    
PYMOL API

    cmd.save(string file, string selection, int state, string format)

NOTES

    The file format is automatically chosen if the extesion is one of
    the supported output formats: pdb, pqr, mol, sdf, pkl, pkla, mmd, out,
    dat, mmod, cif, pov, png, pse, psw, aln, fasta, obj, mtl, wrl, dae, idtf,
    or mol2.

    If the file format is not recognized, then a PDB file is written
    by default.

    For molecular files and where applicable and supported:
    
    * if state = -1 (default), then only the current state is written.

    * if state = 0, then a multi-state output file is written.
    
SEE ALSO

    load, get_model

api: pymol.exporting.save


scene

DESCRIPTION

    "scene" saves and restores scenes.  A scene consists of the camera
    view, all object activity information, all atom-wise visibilities,
    all atom-wise colors, all representations, the global frame index,
    and may contain a text message to display on playback.

USAGE

    scene [key [,action [, message, [ new_key=new-key-value ]]]]

ARGUMENTS

    key = string, new, auto, or *: use new for an automatically
    numbered new scene, use auto for the current scene (if one
    exists), and use * for all scenes (clear and recall actions only).
    
    action = store, recall, insert_after, insert_before, next,
    previous, update, rename, or clear: (default = recall).  If
    rename, then a new_key argument must be explicitly defined.

    message = string: a text message to display with the scene.

    new_key = string: the new name for the scene
    
EXAMPLES

    scene *

    scene F1, store
    scene F2, store, Please note the critical hydrogen bond shown in yellow.

    scene F1
    scene F2

    scene F1, rename, new_key=F5

NOTES

    Scenes F1 through F12 are automatically bound to function keys
    provided that "set_key" has not been used to redefine the behaviour
    of the respective key.
    
SEE ALSO

    view, set_view, get_view

api: pymol.viewing.scene


scene_order

DESCRIPTION

    "scene_order" changes the ordering of scenes.

USAGE

    scene_order names, sort, location

ARGUMENTS

    names = string: a space-separated list of names

    sort = yes or no {default: no}

    location = top, current, or bottom {default: current}

EXAMPLES

    scene_order *,yes             
    scene_order F6 F4 F3 
    scene_order 003 006 004, location=top

PYMOL API

    cmd.scene_order(string names, string sort, string location)

SEE ALSO

    scene

api: pymol.viewing.scene_order


sculpt_activate

DESCRIPTION

    "sculpt_activate" enables sculpting for the given object. The current
    geometry (bond lengths, angles, etc.) of the given state is remembered as
    the reference geometry.

ARGUMENTS

    object = str: name of a single object or "all"

    state = int: object state or 0 for current state {default: 0}

SEE ALSO

    sculpt_iterate, sculpt_deactivate

api: pymol.editing.sculpt_activate


sculpt_deactivate

DESCRIPTION

    "sculpt_deactivate" deactivates sculpting for the given object and
    clears the stored restraints.

ARGUMENTS

    object = str: name of a single object or "all"

SEE ALSO

    sculpt_activate

api: pymol.editing.sculpt_deactivate


sculpt_iterate

DESCRIPTION

    "sculpt_iterate" performs a simple energy minimization of atomic
    coordinates based on the geometry restraints which were defined with
    the "sculpt_activate" invocation and which are selected in the
    "sculpt_field_mask" setting. Sculpting currently supports local
    geometry restraints and vdw repulsion, but no solvation or
    electrostatic effects.

ARGUMENTS

    object = str: name of a single object or "all"

    state = int: object state or 0 for current state {default: 0}

    cycles = int: number of iterations {default: 10}

SEE ALSO

    commands: sculpt_activate, sculpt_deactivate
    settings: "sculpting" setting, all "sculpt_*" settings

api: pymol.editing.sculpt_iterate


sculpt_purge

DESCRIPTION

    "sculpt_purge" is an unsupported feature.

api: pymol.editing.sculpt_purge


select

DESCRIPTION

    "select" creates a named atom selection from a
    selection-expression.

USAGE

    select name, selection [, enable [, quiet [, merge [, state [, domain ]]]]]

ARGUMENTS

    name = a unique name for the selection

    selection = a selection-expression

NOTES

    If a selection-expression with explicit surrounding parethenses is
    provided as the first argument, then the default selection name
    is used as the name argument.

EXAMPLES 

    select chA, chain A
    select ( resn HIS )
    select near142, resi 142 around 5

PYMOL API

    cmd.select(string name, string selection)

SEE ALSO

    delete

api: pymol.selecting.select


set

DESCRIPTION

    "set" changes global, object, object-state, or per-atom settings.

USAGE

    set name [,value [,selection [,state ]]]

ARGUMENTS

    name = string: setting name

    value = string: a setting value {default: 1}

    selection = string: name-pattern or selection-expression
    {default:'' (global)}

    state = a state number {default: 0 (per-object setting)}

EXAMPLES

    set orthoscopic

    set line_width, 3

    set surface_color, white, 1hpv
    
    set sphere_scale, 0.5, elem C

NOTES

    The default behavior (with a blank selection) is global.  If the
    selection is "all", then the setting entry in each individual
    object will be changed.  Likewise, for a given object, if state is
    zero, then the object setting will be modified.  Otherwise, the
    setting for the indicated state within the object will be
    modified.

    If a selection is provided as opposed to an object name, then the
    atomic setting entries are modified.

    The following per-atom settings are currently implemented.  Others
    may seem to be recognized but will have no effect when set on a
    per-atom basis.
    
    * sphere_color
    * surface_color
    * mesh_color
    * label_color
    * dot_color
    * cartoon_color
    * ribbon_color
    * transparency (for surfaces)
    * sphere_transparency
    
    Note that if you attempt to use the "set" command with a per-bond
    setting over a selection of atoms, the setting change will appear
    to take, but no change will be observed.  Please use the
    "set_bond" command for per-bond settings.
    

PYMOL API

    cmd.set(string name, string value, string selection, int state,
            int updates, int quiet)

SEE ALSO

    get, set_bond

api: pymol.setting.set


set_atom_property

DESCRIPTION

    Set an atom-level property

USAGE

    set_atom_property name, value [, selection [, state [, proptype ]]]

ARGUMENTS

    name = string: Name of the property

    value = str/int/float/bool: Value to be set

    selection = string: a selection-expression
    {default: all}

    proptype = int: The type of the property, -1=auto, 1=bool, 2=int,
    3=float, 5=color, 6=str. Type -1 will detect int (digits only), float,
    and bool (true/false/yes/no). {default: -1}

    state = int: Object state, 0 for all states, -1 for current state
    {default: 0}

EXAMPLE

    set_atom_property myfloatprop,  1.23, elem C
    set_atom_property myfloatprop,  1234, elem N, proptype=3
    set_atom_property myboolprop,   TRUE, elem O
    set_atom_property mystrprop,   false, elem O, proptype=6
    set_atom_property mystrprop, One Two, elem C
    iterate all, print(elem, p.all)
    alter all, p.myboolprop = True
    alter all, p.myfloatprop = None # clear

SEE ALSO

    set_property, iterate, alter

api: pymol.properties.set_atom_property


set_bond

DESCRIPTION

    "set_bond" changes per-bond settings for all bonds which exist
    between two selections of atoms.

USAGE

    set_bond name, value, selection1 [, selection2 ]

ARGUMENTS

    name = string: name of the setting

    value = string: new value to use

    selection1 = string: first set of atoms

    selection2 = string: seconds set of atoms {default: (selection1)}

EXAMPLE

    set_bond stick_transparency, 0.7, */n+c+ca+o


NOTES

    The following per-bond settings are currently implemented.  Others
    may seem to be recognized but will currently have no effect when
    set at the per-bond level.
    
    * valence
    * line_width
    * line_color
    * stick_radius
    * stick_color
    * stick_transparency

    Note that if you attempt to use the "set" command with a per-bond
    setting over a selection of atoms, the setting change will appear
    to take, but no change will be observed.
    
PYMOL API

    cmd.set_bond ( string name, string value,
                   string selection1,
                   string selection2,
                   int state, int updates, log=0, quiet=1)

api: pymol.setting.set_bond


set_color

DESCRIPTION

    "set_color" defines a new color using the red, green, and blue
    (RGB) color components.

USAGE

    set_color name, rgb

ARGUMENTS

    name = string: name for the new or existing color

    rgb = list of numbers: [red, green, blue] each and all in the range
    (0.0, 1.0) or (0, 255)
    
EXAMPLES 

    set_color red, [ 1.0, 0.0, 0.0 ]

    set_color yellow, [ 255, 255, 0 ]

NOTES

    PyMOL automatically infers the range based on the input arguments.

    It may be necessary to issue "recolor" command in order to force
    recoloring of existing objects.
    
SEE ALSO

    recolor
    
PYMOL API

    cmd.set_color(string name, list-of-numbers rgb, int mode )

api: pymol.viewing.set_color


set_dihedral

DESCRIPTION

    "set_dihedral" changes the dihedral angle formed between the four
    bonded atoms provided.  The atoms must be acyclic.
    
USAGE

    set_dihedral atom1, atom2, atom3, atom4, angle [, state [, quiet ]]

NOTES

    Because set_dihedral uses the molecular editing capability,
    numbered "pk" atom selections (if any) will be redefined by this
    operation.
    
PYMOL API

    cmd.set_dihedral(string atom1, string atom2, string atom3, string atom4,
                     float angle, int state, int quiet)

api: pymol.editing.set_dihedral


set_geometry

DESCRIPTION

    "set_geometry" changes PyMOL's assumptions about the proper valence
    and geometry of atoms in the selection.

USAGE

    set_geometry selection, geometry, valence

NOTES

    Immature functionality. See code for details.

PYMOL API

    cmd.set_geometry(string selection, int geometry, int valence)

SEE ALSO

    remove, attach, fuse, bond, unbond

api: pymol.editing.set_geometry


set_key

DESCRIPTION

    "set_key" binds a specific python function to a key press.

    New in PyMOL 1.6.1: second argument can also be a string in PyMOL
    command syntax.

USAGE

    set_key key, command

EXAMPLE

    set_key F1, as cartoon, polymer; as sticks, organic

PYMOL API (ONLY)

    cmd.set_key( string key, function fn, tuple arg=(), dict kw={})

PYTHON EXAMPLE

    from pymol import cmd

    def color_blue(object): cmd.color("blue",object)

    cmd.set_key( 'F1' , color_blue, ( "object1" ) )
    // would turn object1 blue when the F1 key is pressed and

    cmd.set_key( 'F2' , color_blue, ( "object2" ) )
    // would turn object2 blue when the F2 key is pressed.

    cmd.set_key( 'CTRL-C' , cmd.zoom )   
    cmd.set_key( 'ALT-A' , cmd.turn, ('x',90) )

KEYS WHICH CAN BE REDEFINED

    F1 to F12
    left, right, pgup, pgdn, home, insert
    CTRL-A to CTRL-Z 
    ALT-0 to ALT-9, ALT-A to ALT-Z

SEE ALSO

    button, alias

api: pymol.controlling.set_key


set_name

DESCRIPTION

    "set_name" changes the name of an object or selection.
    
USAGE

    set_name old_name, new_name
    
PYMOL API

    cmd.set_name(string old_name, string new_name)

api: pymol.editing.set_name


set_property

DESCRIPTION

    Set an object-level property

USAGE

    set_property name, value [, object [, state [, proptype ]]]

ARGUMENTS

    name = string: Name of the property

    value = str/int/float/bool: Value to be set

    object = string: Space separated list of objects or * for all objects
    {default: *}

    proptype = int: The type of the property, -1=auto, 1=bool, 2=int,
    3=float, 5=color, 6=str. Type -1 will detect int (digits only), float,
    and bool (true/false/yes/no). {default: -1}

    state = int: Object state, 0 for all states, -1 for current state
    {default: 0}

EXAMPLE

    fragment ala
    set_property myfloatprop, 1234, ala, proptype=3
    get_property myfloatprop, ala

SEE ALSO

    get_property, get_property_list, set_atom_property

api: pymol.properties.set_property


set_symmetry

DESCRIPTION

    "set_symmetry" defines or redefines the crystal and spacegroup
    parameters for a molecule or map object.

USAGE

    set_symmetry selection, a, b, c, alpha, beta, gamma, spacegroup

NOTES

    The new symmetry will be defined for every object referenced
    by the selection.

PYMOL API

    cmd.set_symmetry(string selection, float a, float b, float c,
          float alpha, float beta, float gamma, string spacegroup)

api: pymol.editing.set_symmetry


set_title

DESCRIPTION

    "set_title" attaches a text string to the state of a particular
    object which can be displayed next to the object name when that
    state is active.  This is useful for display the energies of a set
    of conformers.

USAGE

    set_title object, state, text

PYMOL API

    cmd.set_title(string object, int state, string text)

api: pymol.editing.set_title


set_view

DESCRIPTION

    "set_view" sets viewing information for the current scene,
    including the rotation matrix, position, origin of rotation,
    clipping planes, and the orthoscopic flag.

USAGE

    set_view [ view ] 

EXAMPLE

    set_view (\
        0.999876618,   -0.000452542,   -0.015699286,\
        0.000446742,    0.999999821,   -0.000372844,\
        0.015699454,    0.000365782,    0.999876678,\
        0.000000000,    0.000000000, -150.258514404,\
        11.842411041,   20.648729324,    8.775371552,\
        118.464958191,  182.052062988,    0.000000000 )

PYMOL API

    cmd.set_view(string-or-sequence view)  

SEE ALSO

    get_view

api: pymol.viewing.set_view


show

DESCRIPTION

    "show" turns on representations for objects and selections.

USAGE

    show [ representation [, selection ]]

ARGUMENTS

    representation = lines, spheres, mesh, ribbon, cartoon, sticks,
       dots, surface, labels, extent, nonbonded, nb_spheres, slice,
       extent, slice, dashes, angles, dihedrals, cgo, cell, callback,
       or everything

    selection = string: a selection-expression or name-pattern

NOTES

    With no arguments, "show" alone turns on lines for all bonds and
    nonbonded for all atoms in all molecular objects.

EXAMPLES

    show
    show ribbon
    show lines, (name CA+C+N)

SEE ALSO

    hide, enable, disable

api: pymol.viewing.show


skip

DESCRIPTION

    "skip" delimits a block of commands that are skipped instead of
    being executed.

EXAMPLE


    skip

    # the following command will not be executed
    color blue, all
    
    skip end

NOTES

    If the "skip" command is commented out, the subsequent "skip end"
    can be left in place, and will have no effect upon execution of
    subsequent commands.
    
SEE ALSO

    abort, embed, python

api: pymol.helping.skip


slice_new

DESCRIPTION

    "slice_map" creates a slice object from a map object.

USAGE

    slice_map name, map, [opacity, [resolution, [state, [source_state]]]]

ARGUMENTS

    name = the name for the new slice object.

    map = the name of the map object to use for computing the slice.

    opacity = opacity of the new slice (default=1)

    resolution = the number of pixels per sampling (default=5)

    state = the state into which the object should be loaded (default=1)
        (set state=0 to append new mesh as a new state)

    source_state = the state of the map from which the object should be loaded (default=0)
    
SEE ALSO

    isomesh, isodot, load

api: pymol.creating.slice_new


smooth

DESCRIPTION

    "smooth" performs a window average of coordinate states.  

USAGE

    smooth [ selection [, passes [, window [, first [, last [, ends]]]]]]

ARGUMENTS

    ends = 0 or 1: controls whether or not the end states are also smoothed
    using a weighted asymmetric window

NOTES

    This type of averaging is often used to suppress high-frequency
    vibrations in a molecular dynamics trajectory.

    This function is not memory efficient.  For reasons of
    flexibility, it uses two additional copies of every atomic
    coordinate for the calculation.  If you are memory-constrained in
    visualizing MD trajectories, then you may want to use an external
    tool such as ptraj to perform smoothing before loading coordinates
    into PyMOL.

SEE ALSO

    load_traj

api: pymol.editing.smooth


sort

DESCRIPTION

    "sort" reorders atoms in the structure.  It usually only necessary
    to run this routine after an "alter" command which has modified the
    names of atom properties.  Without an argument, sort will resort
    all atoms in all objects.

USAGE

    sort [object]

PYMOL API

    cmd.sort(string object)

SEE ALSO

    alter

api: pymol.editing.sort


space

DESCRIPTION

    "space" selects a color palette (or color space).
    
USAGE

    space space [, gamma]

ARGUMENTS

    space = rgb, cmyk, or pymol: {default: rgb}

    gamma = floating point gamma transformation
    
EXAMPLES

    space rgb
    space cmyk
    space pymol

NOTES

    Whereas computer displays use the RGB color space, computer
    printers typically use the CMYK color space.  The two spaces are
    non-equivalent, meaning that certain RGB colors cannot be
    expressed in the CMYK space and vice-versa.  And as a result,
    molecular graphics images prepared using RGB often turn out poorly
    when converted to CMYK, with purplish blues or yellowish greens.
    
    "space cmyk" forces PyMOL to restrict its use of the RGB color
    space to subset that can be reliably converted to CMYK using
    common tools such as Adobe Photoshop.  Thus, what you see on the
    screen is much closer to what you will get in print.

    Analog video systems as well as digital video compression codecs
    based on the YUV color space also have incompatibilities with RGB.
    Oversaturated colors usually cause the most problems.

    Although PyMOL lacks "space yuv", "space pymol" will help PyMOL
    avoid oversaturated colors can cause problems when exporting
    animations to video.

PYMOL API

    cmd.space(string space, float gamma)
    
SEE ALSO

    color

api: pymol.importing.space


spawn

DESCRIPTION

    "spawn" launches a Python script in a new thread which will run
    concurrently with the PyMOL interpreter. It can be run in its own
    namespace (like a Python module, default), a local name space, or
    in the global namespace.

USAGE

    spawn file [, namespace ]

NOTES

    The default namespace for spawn is "module".

    The best way to spawn processes at startup is to use the -l option
    (see "help launching").

SEE ALSO

    run

api: pymol.parsing.spawn


spectrum

DESCRIPTION

    "spectrum" colors atoms with a spectrum of colors based on an atomic
    property.
    
USAGE

    spectrum [expression [, palette [, selection [, minimum [, maximum [, byres ]]]]]]

ARGUMENTS

    expression = count, b, q, pc or properties["key"]: respectively, atom
    count, temperature factor, occupancy, partial charge or a user defined
    numeric atom property {default: count}
    
    palette = string: palette name or space separated list of colors
    {default: rainbow}

    selection = string: atoms to color {default: (all)}

    minimum = float: {default: None (automatic)}

    maximum = float: {default: None (automatic)}

    byres = integer: controls whether coloring is applied per-residue {default: 0}

EXAMPLES

    spectrum b, blue_red, minimum=10, maximum=50

    spectrum count, rainbow_rev, chain A, byres=1

    spectrum properties["some_score"], red yellow white

NOTES

    Available palettes include:

       blue_green blue_magenta blue_red blue_white_green
       blue_white_magenta blue_white_red blue_white_yellow blue_yellow
       cbmr cyan_magenta cyan_red cyan_white_magenta cyan_white_red
       cyan_white_yellow cyan_yellow gcbmry green_blue green_magenta
       green_red green_white_blue green_white_magenta green_white_red
       green_white_yellow green_yellow green_yellow_red magenta_blue
       magenta_cyan magenta_green magenta_white_blue
       magenta_white_cyan magenta_white_green magenta_white_yellow
       magenta_yellow rainbow rainbow2 rainbow2_rev rainbow_cycle
       rainbow_cycle_rev rainbow_rev red_blue red_cyan red_green
       red_white_blue red_white_cyan red_white_green red_white_yellow
       red_yellow red_yellow_green rmbc yellow_blue yellow_cyan
       yellow_cyan_white yellow_green yellow_magenta yellow_red
       yellow_white_blue yellow_white_green yellow_white_magenta
       yellow_white_red yrmbcg

PYMOL API

    def spectrum(string expression, string palette,
                 string selection, float minimum, float maximum,
                 int byres, int quiet)

api: pymol.viewing.spectrum


spheroid

DESCRIPTION

    "spheroid" averages trajectory frames together to create
    an ellipsoid-like approximation of the actual anisotropic
    motion exhibited by the atom over a series of trajectory frames.

USAGE

    spheroid object,average

    average = number of states to average for each resulting spheroid state

api: pymol.experimenting.spheroid


splash

UNDOCUMENTED

api: pymol.commanding.splash


split_chains

DESCRIPTION

    Create a single object for each chain in selection

SEE ALSO

    split_states

api: pymol.editing.split_chains


split_states

DESCRIPTION

    "split_states" separates a multi-state molecular object into a set
    of single-state molecular objects.

USAGE

    split_states object [, first [, last [, prefix ]]]
    
EXAMPLE

    load docking_hits.sdf
    split_states docking_hits, prefix=hit
    delete docking_hits
    
SEE ALSO

    join_states

api: pymol.editing.split_states


stereo

DESCRIPTION

    "stereo" activates or deactives stereo mode.

USAGE

    stereo [toggle]

ARGUMENTS

    toggle = on, off, crosseye, walleye, quadbuffer, sidebyside, or geowall
    
EXAMPLES

    stereo on
    stereo off
    stereo crosseye

NOTES

    "quadbuffer" is the default stereo mode if hardware stereo is available.
    otherwise, "crosseye" is the default.

PYMOL API

    cmd.stereo(string toggle)

api: pymol.viewing.stereo


super

DESCRIPTION

        "super" performs a residue-based pairwise alignment followed by a
        structural superposition, and then carries out zero or more cycles
        of refinement in order to reject outliers.

USAGE 

        super mobile, target [, object=name ]

NOTES

        By adjusting various parameters, the nature of the initial
        alignment can be modified to include or exclude various factors
        including sequence similarity, main chain path, secondary &
        tertiary structure, and current coordinates.

EXAMPLE

        super protA////CA, protB////CA, object=supeAB

SEE ALSO

        align, pair_fit, fit, rms, rms_cur, intra_rms, intra_rms_cur

api: pymol.fitting.super


symexp

DESCRIPTION

    "symexp" creates all symmetry-related objects for the specified
    object that occur within a cutoff about an atom selection.

USAGE

    symexp prefix, object, selection, cutoff

NOTES

    The newly objects are labeled using the prefix provided along with
    their crystallographic symmetry operation and translation.

SEE ALSO

    load

api: pymol.creating.symexp


symmetry_copy

DESCRIPTION

    "symmetry_copy" copies symmetry information from one object to another.

USAGE

    symmetry_copy source_name, target_name, source_state, target_state

NOTES

    Maps support accessing and setting states other than the first,
    but molecular objects do not.

    New in PyMOL v1.5.

PYMOL API

    cmd.symmetry_copy(source_name, target_name, source_state, target_state,
        target_undo, log, quiet)

api: pymol.editing.symmetry_copy


system

DESCRIPTION

    "system" executes a command in a subshell under Unix or Windows.

USAGE

    system command 

PYMOL API

    cmd.system(string command,int async=0)

NOTES

    async can only be specified from the Python level (not the command language)

    if async is 0 (default), then the result code from "system" is returned in r

    if async is 1, then the command is run in a separate thread whose object is
    returned

SEE ALSO

    ls, cd, pwd

api: pymol.externing.system


toggle

DESCRIPTION

    "toggle" toggles the visibility of a representation within a
    selection.
    
USAGE

    toggle [ representation [, selection ]]

ARGUMENTS

    representation = string: named representation {default: lines}

    selection = string: atom selection {default: all}

NOTES

    If the representation is enabled for any atom in the selection, it will
    be turned off.

PYMOL API

    cmd.toggle(string representation, string selection)

SEE ALSO

    show, hide

api: pymol.viewing.toggle


torsion

DESCRIPTION

    "torsion" rotates the torsion on the bond currently
    picked for editing.  The rotated fragment will correspond
    to the first atom specified when picking the bond (or the
    nearest atom, if picked using the mouse).

USAGE

    torsion angle

PYMOL API

    cmd.torsion( float angle )

SEE ALSO

    edit, unpick, remove_picked, cycle_valence

api: pymol.editing.torsion


translate

DESCRIPTION

    "translate" translates the atomic coordinates of atoms in a
    selection.  Alternatively, is modifies the matrix associated with
    a particular object or object-state.

USAGE

    translate vector [, selection [, state [, camera [, object ]]]]

ARGUMENTS

    vector = float vector: translation vector

    selection = string: atoms whose coordinates should be modified {default: all}

    state > 0: only the indicated state is modified

    state = 0: all states are modified

    state = -1: only current state is modified {default}

    camera = 0 or 1: is the vector in camera coordinates? {default: 1 (yes)}

    object = string: object name (only if rotating object matrix) {default: None}


PYMOL API

    cmd.translate(list vector, string selection, int state, int
                  camera, string object)

EXAMPLES

    translate [1,0,0], name CA

NOTES

    "translate" can be used to translate the atomic coordinates of a
    molecular object.  Behavior differs depending on whether or not
    the "object" parameter is specified.

    If object is None, then translate translates atomic coordinates
    according to the vector provided for the selection and in the state
    provided.  All representation geometries will need to be
    regenerated to reflect the new atomic coordinates.

    If object is set to an object name, then selection is ignored and
    instead of translating the atomic coordinates, the object's
    overall representation display matrix is modified.  This option is
    for use in animations only.

    The "camera" option controls whether the camera or the model's
    axes are used to interpret the translation vector.

api: pymol.editing.translate


turn

DESCRIPTION

    "turn" rotates the camera about one of the three primary axes,
    centered at the origin.

USAGE

    turn axis, angle

EXAMPLES

    turn x, 90
    turn y, 45

PYMOL API

    cmd.turn(string axis, float angle)

SEE ALSO

    move, rotate, translate, zoom, center, clip

api: pymol.viewing.turn


unbond

DESCRIPTION

    "unbond" removes all bonds between two selections.

USAGE

    unbond atom1,atom2

ARGUMENTS

    atom1 = string {default: (pk1)}

    atom2 = string {default: (pk2)}

PYMOL API

    cmd.unbond(selection atom1, selection atom2)

SEE ALSO

    bond, fuse, remove_picked, attach, detach, replace

api: pymol.editing.unbond


undo

DESCRIPTION

    "undo" restores the previous conformation of the object currently
    being edited.

USAGE

    undo

SEE ALSO

    redo, push_undo

api: pymol.editing.undo


ungroup

DESCRIPTION

    "ungroup" removes an object from a group object, returning it to
    the top level.

USAGE

    ungroup name


SEE ALSO

    group

api: pymol.creating.ungroup


uniquify

DESCRIPTION

    Make `identifier` unique with respect to reference selection.

ARGUMENTS

    identifier = str: atom identifier (chain, segi, etc.)

    selection = str: atom selection to modify

    reference = str: atom selection whose identifiers must not be
    present in the first selection {default: !selection}

EXAMPLE

    fetch 1a00 1hbb, async=0
    uniquify chain, 1hbb
    # 1hbb now has chains E,F,G,H

api: pymol.editing.uniquify


unmask

DESCRIPTION

    "unmask" reverses the effect of "mask" on the indicated atoms.

PYMOL API

    cmd.unmask( string selection="(all)" )

USAGE

    unmask (selection)

SEE ALSO

    mask, protect, deprotect, mouse

api: pymol.controlling.unmask


unpick

DESCRIPTION

    "unpick" deletes the special "pk" atom selections (pk1, pk2, etc.)
    used in atom picking and molecular editing.

USAGE

    unpick

PYMOL API

    cmd.unpick()

SEE ALSO

    edit

api: pymol.editing.unpick


unset

DESCRIPTION

    "unset" clear non-global settings and zeros out global settings.

    WARNING: The behavior for global settings is subject to change.
    To set a setting to zero, do "set settingname, 0".

USAGE

    unset name [,selection [,state ]]

EXAMPLE

    unset orthoscopic

    unset surface_color, 1hpv

    unset sphere_scale, elem C
    
NOTES

    If selection is not provided, unset changes the named global
    setting to a zero or off value.

    If a selection is provided, then "unset" undefines per-object,
    per-state, or per-atom settings.

PYMOL API

    cmd.unset(string name, string selection, int state, int updates,
                int log)

SEE ALSO

    set, set_bond

api: pymol.setting.unset


unset_bond

DESCRIPTION

    "unset_bond" removes a per-bond setting for a given set of bonds.
    
USAGE

    unset name [,selection [, selection [,state ]]]

api: pymol.setting.unset_bond


unset_deep

DESCRIPTION

    Unset all object, object-state, atom, and bond level settings.

    Note: Does currently NOT unset atom-state level settings. Check for
    atom-state level settings with:
    PyMOL> iterate_state 1, *, print list(s)
    Unset e.g. atom-state level "label_screen_point" (index 728) with:
    PyMOL> alter_state 1, *, del s[728]

ARGUMENTS

    settings = str: space separated list of setting names or empty string
    for all settings {default: }

    object = str: name of one object or * for all objects {default: *}

api: pymol.setting.unset_deep


update

DESCRIPTION

    "update" transfers coordinates from one selection to another.
USAGE

    update (target-selection),(source-selection)

EXAMPLES

    update target,(variant)

NOTES

    Currently, this applies across all pairs of states.  Fine
    control will be added later.

SEE ALSO

    load

api: pymol.editing.update


util.cbab

Wrapper around "color atomic"

api: pymol.util.cbab


util.cbac

Wrapper around "color atomic"

api: pymol.util.cbac


util.cbag

Wrapper around "color atomic"

api: pymol.util.cbag


util.cbak

Wrapper around "color atomic"

api: pymol.util.cbak


util.cbam

Wrapper around "color atomic"

api: pymol.util.cbam


util.cbao

Wrapper around "color atomic"

api: pymol.util.cbao


util.cbap

Wrapper around "color atomic"

api: pymol.util.cbap


util.cbas

Wrapper around "color atomic"

api: pymol.util.cbas


util.cbaw

Wrapper around "color atomic"

api: pymol.util.cbaw


util.cbay

Wrapper around "color atomic"

api: pymol.util.cbay


util.cbc

Color all chains a different color

api: pymol.util.cbc


util.chainbow

Color all chains in rainbow

api: pymol.util.chainbow


util.cnc

Wrapper around "color atomic"

api: pymol.util.cnc


util.rainbow

Legacy spectrum coloring routine. Don't use.

    Use instead: spectrum

api: pymol.util.rainbow


util.ss

Legacy secondary structure assignment routine. Don't use.

    Use instead: dss

api: pymol.util.ss


valence

DESCRIPTION

    "valence" modifies the valences of all existing bonds formed
    between two atom selections.
    
USAGE

    valence 2, (name C), (name O)

PYMOL API

    cmd.valence(string selection1, selection2)

SEE ALSO

    unbond, fuse, attach, replace, remove_picked

api: pymol.editing.valence


vdw_fit

DESCRIPTION

    "vdw_fit" is an unsupported feature.

api: pymol.editing.vdw_fit


view

DESCRIPTION

    "view" saves and restore camera views.

USAGE

    view key [, action [, animate]]
    
ARGUMENTS

    key = string or *

    action = store or recall: {default: recall}

NOTES

    Views F1 through F12 are automatically bound to function keys
    provided that "set_key" has not been used to redefine the
    behaviour of the respective key, and that a "scene" has not been
    defined for that key.

EXAMPLES

    view 0, store
    view 0

PYMOL API

    cmd.view(string key, string action)

SEE ALSO

    scene, set_view, get_view

api: pymol.viewing.view


viewport

DESCRIPTION

    "viewport" changes the size of the graphics display area.

USAGE

    viewport width, height

PYMOL API

    cmd.viewport(int width, int height)

api: pmg_qt.pymol_qt_gui.viewport


volume

DESCRIPTION

    "volume" creates a volume object from a map object.

USAGE

    volume name, map [, ramp [, selection [, buffer [, state [, carve ]]]]]

ARGUMENTS

    name = the name for the new volume object.

    map = the name of the map object to use for computing the volume.

    ramp = str: named color ramp {default: }

    selection = an atom selection about which to display the mesh with
        an additional "buffer" (if provided).

    carve = a radius about each atom in the selection for which to
        include density. If "carve" is not provided, then the whole
        brick is displayed.

NOTES

    If the volume object already exists, then the new volume will 
    overwrite the existing object.

EXAMPLE

    fetch 1oky, async=0
    fetch 1oky, type=2fofc, async=0
    volume 1okyVol, 1oky_2fofc

SEE ALSO

    map_new, isosurface, isomesh, volume_color, volume_ramp_new

api: pymol.creating.volume


volume_color

DESCRIPTION

    Set or get the volume colors.

ARGUMENTS

    name = str: volume object name

    ramp = str, list or empty: named ramp, space delimited string or list
    with (x, color, alpha, ...) or (x, r, g, b, alpha, ...) values. If empty, get
    the current volume colors.

EXAMPLE

    fetch 1a00, map, type=2fofc
    volume vol, map
    volume_color vol, .8 cyan 0. 1. blue .3 2. yellow .3

api: pymol.colorramping.volume_color


volume_panel

DESCRIPTION

    Open an interactive volume ramp panel

ARGUMENTS

    name = str: name of volume object

api: pymol.colorramping.volume_panel


volume_ramp_new

DESCRIPTION

    Register a named volume ramp which can be used as a preset
    when creating or coloring volumes. The name will appear in the
    internal menu at "A > volume" and "C".

ARGUMENTS

    name = string: name of the new ramp

    ramp = list: space delimited list of value, color, alpha

EXAMPLE

    volume_ramp_new pink1sigma, \
       0.9 violet 0.0 \
       1.0 magenta 0.3 \
       1.5 pink 0.0

SEE ALSO

    volume, volume_color

api: pymol.colorramping.volume_ramp_new


window

DESCRIPTION

    "window" controls the visibility of PyMOL's output window

USAGE

    window [ action [, x [, y [, width [, height ]]]]]

PYMOL API

    cmd.window(string action, int x, int y, int width, int height)

api: pymol.viewing.window


wizard

DESCRIPTION

    "wizard" launches on of the built-in wizards.  There are special
    Python scripts which work with PyMOL in order to obtain direct user
    interaction and easily peform complicated tasks.

USAGE

    wizard name

PYMOL API

    cmd.wizard(string name)

EXAMPLE

    wizard distance  # launches the distance measurement wizard

api: pymol.wizarding.wizard


zoom

DESCRIPTION

    "zoom" scales and translates the window and the origin to cover the
    atom selection.

USAGE

    zoom [ selection [, buffer [, state [, complete [, animate ]]]]]
    
EXAMPLES

    zoom 
    zoom complete=1
    zoom 142/, animate=3
    zoom (chain A)

ARGUMENTS

    selection = string: selection-expression or name pattern {default: all}

    buffer = float: distance  {default: 0}
    
    state = 0: uses all coordinate states {default}
    
    state = -1: uses only coordinates for the current state
    
    state > 0: uses coordinates for a specific state

    complete = 0 or 1: will insure no atoms centers are clipped

    animate < 0: uses the default animation duration
    
    animate = 0: no animation
    
    animate > 0: animates using the provided duration in seconds
    
PYMOL API

    cmd.zoom(string selection, float buffer, int state, int complete,
             int animate)

NOTES

    The zoom command normally tries to guess an optimal zoom level for
    visualization, balancing closeness against occasional clipping of
    atoms out of the field of view.  You can change this behavior by
    setting the complete option to 1, which will guarantee that the
    atom positions for the entire selection will fit in the field of
    an orthoscopic view.

    To absolutely prevent clipping, you may also need to add an
    additional buffer (typically 2 A) to account for graphical
    representations which extend beyond the atom coordinates.  

SEE ALSO

    origin, orient, center

api: pymol.viewing.zoom