Beginning with incentive PyMOL 1.6, arbitrary object level and atom level properties are supported. Now, for each object and each atom you can possibly have an arbitrary dictionary associated with each.


cmd.set("load_object_props_default", "*")
cmd.load("", "caffeine", format="sdf")
cmd.wizard("message", "Vol: %.1f" % cmd.get_property("PUBCHEM_SHAPE_VOLUME", "caffeine"))

Object Level Properties

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

Atom Level Properties

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

Selection Language


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
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