PyMOL Documentation

cmd.set("load_object_props_default", "*")
cmd.load("http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=2519&disopt=3DSaveSDF", "caffeine", format="sdf")
cmd.wizard("message", "Vol: %.1f" % cmd.get_property("PUBCHEM_SHAPE_VOLUME", "caffeine"))

Loading from files:

load abc.sdf, object_props=*

set load_object_props_default, *
load abc.sdf

Querying from the command line:

get_property_list abc
get_property some_name, abc

Loading from files:

load abc.mae, atom_props=*

set load_atom_props_default, *
load abc.mae

Querying from the command line:

iterate abc, print(properties["some_name"])  # dictionary notation
iterate abc, print(properties.some_name)     # dot notation
iterate abc, print(p["some_name"])           # shortcut
iterate abc, print(p.some_name)
iterate abc, print(properties.all)           # dictionary of all properties

Coloring by numeric property value:

spectrum properties.some_name, blue yellow red

Scaling a setting by an atom property:

stored.values = []
iterate all, stored.values.append(float(p["some_value"]))
stored.v_min = min(stored.values)
stored.v_range = max(stored.values) - stored.v_min
alter all, s["transparency"] = (float(p["some_value"]) - stored.v_min) / stored.v_range

Numeric:

select mysele, p.some_value = 3
select mysele, p.some_value > 2.4

String, supports matching against sets with “+”:

select myseleA,    p.some_value in A
select myseleAorB, p.some_value in A+B