Granzyme B Peptide Hydrolysis Movie

Example with independent moving objects and animation via object flipping.

Click here to view the resulting movie using QuickTime.

The inputs to this movie consist of the following PDB files, constructed using the 1iau.pdb PDB entry for Granzyme B.

• step1_docked_complex.pdb
• step2_peptide_adduct.pdb
• step3_acyl_enzyme.pdb
• step4_water_adduct.pdb
• step5_free_enzyme.pdb

The first script loads all of the required structures structures and breaks them down into a series of independent objects suitable for constructing the movie.

# PyMOL script: load.pml

load step1_docked_complex.pdb, enzyme
load step2_peptide_adduct.pdb, step2_enz
load step3_acyl_enzyme.pdb, step3_enz
load step4_water_adduct.pdb, step4_enz
load step5_free_enzyme.pdb, step5_enz

# ignore glycosylation for now

remove c//

extract step1_sub, /enzyme//B
create step2_adduct, /step2_enz//B extend 1, extract=/step2_enz//B
create step3_adduct, /step3_enz//B extend 1, extract=/step3_enz//B
create step4_adduct, /step4_enz//B extend 1, extract=/step4_enz//B
extract step5_product, /step5_enz//B

extract step3_product, bymol /step3_adduct//B/SER`406/CA

set surface_quality, 1

order *,sort=1

dele *_enz

The second script does all of the rest of the work to define the movie. Note that this script is designed to be run iteratively (via @movie.pml) so that the user can make a change, rerun the script, and immediately see the effect.

# PyMOL script: movie.pml

# set representations and coloring

as sticks
as surface, enzyme

# green carbons

util.cbag

# white enzyme

color white, enzyme

# with red active-site nucleophile

color oxygen, enzyme///ser`195/OG

# turn off everything

disable

# top-down camera view (frame of reference for translations)

set_view (\
     0.690281689,    0.688584030,    0.222161561,\
    -0.576666951,    0.709035158,   -0.405857205,\
    -0.436990112,    0.152041912,    0.886522174,\
     0.000079889,   -0.000218283,  -79.604537964,\
    10.085126877,   36.368568420,   66.158187866,\
    51.506359100,  107.684165955,    0.000000000 )

# adjust lighting and color saturation

space pymol
set light, [0.1, 0.2, -1]
set reflect, 0.425
set specular_intensity, 0.25
set stick_radius, 0.4
bg white

# reset everything (in case the script was run before)

mset
mview reset, object=step1_sub
mview reset, object=step3_product
mview reset, object=step5_product

reset object=step1_sub
reset object=step3_product
reset object=step5_product

rewind

# start defining the movie...

# pause

madd 1 x30
mdo 1: disable; enable enzyme step1_sub

# move substrate in

start = cmd.count_frames()
madd 1 x120
stop = cmd.count_frames()

cmd.mview("store", stop, object="step1_sub")

translate [0,-0.7,8], object=step1_sub
cmd.mview("store", (start+stop)/2,object="step1_sub")

translate [0,-17,4], object=step1_sub
cmd.mview("store", start, object="step1_sub")
cmd.mview("store", 1, object="step1_sub")

mview interpolate, object=step1_sub

# pause

madd 1 x30

# show adduct

n_frame = cmd.count_frames()
cmd.mdo(n_frame, "disable step1_sub; enable step2_adduct")

# pause

madd 1 x30

# release c-terminal product

n_frame = cmd.count_frames()
cmd.mdo(n_frame, "disable step2_*; enable step3_*")
cmd.mview("store", n_frame,object="step3_product")

# pause

madd 1 x30

# remove c-terminal product

start = cmd.count_frames() + 1
madd 1 x90
stop = cmd.count_frames()

cmd.mview("store", start, object="step3_product")

translate [4,-20,12], object=step3_product
cmd.mview("store", stop, object="step3_product")

mview interpolate, object=step3_product

# pause

madd 1 x30

# show water adduct

n_frame = cmd.count_frames()
cmd.mdo(n_frame, "disable step3_add; enable step4_*")

# pause

madd 1 x30

# show n-terminal product & free enzyme

n_frame = cmd.count_frames()
cmd.mdo(n_frame, "disable step4_*; enable step5_*")
cmd.mview("store", start,object="step5_product")

# pause

madd 1 x30

# remove n-terminal product

start = cmd.count_frames() + 1
madd 1 x90
stop = cmd.count_frames()

cmd.mview("store", start,object="step5_product")

translate [0,-0.7,8], object=step5_product
cmd.mview("store", (start+stop)/2, object="step5_product")

translate [-3,-17,4], object=step5_product
cmd.mview("store", stop, object="step5_product")

mview interpolate, object=step5_product

# set the final camera view

set_view (\
     0.662352204,    0.712388158,    0.231917903,\
    -0.570117116,    0.680115402,   -0.460874110,\
    -0.486055434,    0.173040211,    0.856625080,\
     0.000105150,   -0.000141161, -108.809425354,\
     4.648024559,   31.749435425,   64.498596191,\
    80.722877502,  136.900558472,    0.000000000 )

# rewind and play the movie without looping

rewind
unset movie_loop
mplay

The movie was exported from MacPyMOL with ray tracing enabled and using the QuickTime Animation codec. The resulting file was then recompressed using the QuickTime H.264 codec.

The PDB files and scripts can be downloaded as a ZIP archive: granzyme_hydrolysis.zip.

Example Animations