Re: [PyMOL] exporting surfaces
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: http://sourceforge.net/mailarchive/message.php?msg_id=5856368 http://sourceforge.net/mailarchive/message.php?msg_id=5933822 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. Regards, Chris Chris Want Research Computing Support Computing Network Services University of Alberta Tel: 1-780-492-9418
RE: [PyMOL] Swissprot
Jules, 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... model=cmd.get_model(object-name) for atom in model.atom: print atom.name, atom.chain etc. PyMOL's C code isn't particularly object-oriented -- there is no class which encapsulates the PDB parser. Cheers, Warren -- mailto:war...@delsci.com 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- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Jules Jacobsen Sent: Monday, October 18, 2004 6:41 AM To: pymol-users@lists.sourceforge.net 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, Jules --- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] residues with no bound
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