Re: [PyMOL] exporting surfaces

2004-10-20 Thread C Want

Subject: [PyMOL] exporting surfaces

Dear Pymol users,

Does anyone know if there is a way to export surfaces into a file format
suitable for import into 3D modellers (ie. Blender, 3DSMax, Lightwave, etc)?
For that matter, is it possible at all to export anything in pymol?

Hi Peter,

I wrote a cheap hack a while back to produce STL output for the 
Connolly surfaces in pymol to help send some models to a 3D printer.

Please see these previous messages for a 'patch' and some pictures:

We have some 3D printer users in our Biochemistry department that
still use this hack to get their models out of pymol.

I am also a blender developer (I'm supposed to work on the animation
tools, but I also occasionally add features to help with my work).
I added native STL import/export to blender a few versions ago... so
this might be one way to get your models into blender. The only problem
with this is that the STL format does not have support for colors,
so this is only a good solution if you are solely interested in
the shape of your surfaces. I think my 'patch' could easily be 
modified a bit to create a user-crufted file format for exporting the
colors with the geometry, and then python scripting in blender 
could be used to read this format (as Scott alluded to). This is the 
approach I use to get models out of VTK and into blender.


Chris Want
Research Computing Support
Computing  Network Services
University of Alberta
Tel: 1-780-492-9418

RE: [PyMOL] Swissprot

2004-10-20 Thread Warren DeLano

Right now (and for the foreseeable future) PyMOL's sequence viewer shows
actual atoms in an object (whether or not they have coordinates).  There
isn't currently any way to retrieve that information other than by looking
at atoms...

for atom in model.atom:
   print, atom.chain


PyMOL's C code isn't particularly object-oriented -- there is no class which
encapsulates the PDB parser.


Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
400 Oyster Pt. Blvd., Ste 213
South San Francisco, CA 94080
(650)-346-1154  Fax:(650)-593-4020

 -Original Message-
 [] On Behalf Of 
 Jules Jacobsen
 Sent: Monday, October 18, 2004 6:41 AM
 Subject: [PyMOL] Swissprot
 Hello List,
 I'm trying to make a plugin which will load various features 
 from a swissprot entry onto a model loaded in PyMol but need 
 to know a few things such as:
 Where are the sequences of the models stored in pymol and how 
 do I retrieve them?
 Are these taken from the ATOM or SEQRES sections of the PDB file?
 Is there a PDB parser class somewhere for reading in the PDB files?
 I had a browse through the pymol directory but couldn't find 
 anything which looked like the above. I'm still very new to 
 python so the chances are I have missed it.
 many thanks,
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[PyMOL] residues with no bound

2004-10-20 Thread Mario Sanches

Hi Pymolers

I have a pdb file with two subsequent double conformation residues. When 
I load this on pymol those two residues are not bound. Is there any 
special command I have to use to bound then in this case?

Thanks in advance.

Mario sanches