RE: [PyMOL] multiple MODEL files

[DeLano, W. <wa...@su...>]

> From: Eckhart Guth=F6hrlein=20

> I'm trying to use pymol for the display of pdb files=20
> containing multiple=20
> models using the MODEL card. Indeed, pymol reads in all=20
> models in the file.
> Currently, I'm able to switch between them using the frame=20
> command. Is=20
> there a different way to do this? Something like next_model or=20
> prev_model or show_model ...?
> Furthermore, I tried to use the selection command to access models.
=20
The model operation in the selection command allows you to select =
objects by number -- not models in the sense of multi-model PDB files.  =
The first PDB file you load is model 1, the second is model 2, etc.  =
Sorry for the confusion.  Model was a bad choice in terminology and =
should be replaced with an "object" operator instead.  However, the =
chemical python package uses "model" instead of object, so it's probably =
a hopeless case.

PyMOL treats multi-model PDB files like trajectories, in that each model =
is one state of the trajectory.  You can display them as a series of =
frames as you were doing.  You can use the left and right arrow keys to =
iterate through, or the forward and back commands, or press the play =
button.  You can use "mset" to display states in a different order, etc. =


> color red,(model 10)
>=20
> leads to
>=20
> SelectorSelect1-Error: Invalid Model
>   PyMOL: abrupt program termination

That's a flat-out bug.  Thanks for finding it. =20

> although model 10 exists and has been read in, as shown before by the=20
> message

As I indicated above, model/object 10 doesn't actually exist, but PyMOL =
certainly shouldn't crash...I'll fix that.

> How to access models in an atom selection?

You can't address atoms individually in one model or another without =
breaking them into separate objects.  You can do this using a Python =
loop and use the create command after loading the model file.

When you create an atom selection, you are essentially selecting all =
states of those atoms.  However, many commands take a "state" argument, =
which is the 1-based index for which state you wish to operate on for =
the atom selection.  This is what allows you to change the conformations =
of atoms in a particular state, for instance.  NOTE the PyMOL's atom =
selections can span any number of objects...

> Another question: Is there a way to list details about the currently=20
> available objects? Like sequence, secondary structure, how many=20
> models/chains/ etc.? And the current properties like colour,=20
> charge etc.=20
> of an atom selection? I just browsed the manual very quickly,=20
> so sorry=20
> if I overlooked the information.

The manual stinks.  Some volunteer with more time than myself needs to =
team up with me to create a decent manual -- but one can't complain too =
much about free software.  I can think of more than one company that =
will sell you an expensive closed-source license similar packages, and =
still not provide you with a decent manual.  If you prefer DeLano =
Scientific's open-source approach, then be sure to support it with =
effort or funding.

The key commands are "alter", "alter_state", "iterate", and "label" -- =
and they represent the heart of PyMOL's built-in atom property =
manipulation capability.  However, there are a bunch of other commands =
for manipulating coordinates and geometries.

iterate (all),print name
iterate (all),print color
iterate (all),print partial_charge
iterate (name ca),print resn,resi,s

alter (all),vdw=3Dvdw*0.5
alter (all),resi=3Dint(resi)+10
alter (chain E),chain=3D'C'

alter_state 1,(all),x=3Dx+2.0

label (name ca),resi

label (all),name
label (all),"%1.2f"%vdw

In all cases, a Python expression is evaluated for each atom in the =
selection.

See "help iterate", etc., but note that the docs are incomplete.  To see =
all the properties which can be printed or altered, load a model and =
then try:

iterate (index 1),print locals().keys()

Note that you can also obtain and manipulate a complete copy of any =
model (erg, object) at the Python level, using Python code like:

from pymol import cmd

m =3D cmd.get_model('old')
m.atom[0].name=3D'C1'
cmd.load_model(m,'new')

Cheers,
Warren