Re: [PyMOL] loop through pymol models

Hi Matthias, use this: cmd.get_object_list() also similar: cmd.get_names() cmd.get_names_of_type(object:molecule) http://pymolwiki.org/index.php/Get_names http://pymolwiki.org/index.php/Get_names_of_type Cheers, Thomas Matthias Schmidt wrote, On 03/16/12 11:54: Hi, I would like to have

[PyMOL] PyMOL Selector

Dear PyMOL List What is the segi-identifier? Thanks for your answer. Martin -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure

Re: [PyMOL] PyMOL Selector

Hi Martin, 'segi' is the segment identifier (http://deposit.rcsb.org/adit/docs/pdb_atom_format.html). Just another hierarchical step, like chains, in the PDB. Cheers, -- Jason On Fri, Mar 16, 2012 at 10:51 AM, Martin Hediger ma@bluewin.ch wrote: Dear PyMOL List What is the

[PyMOL] color_by_mutation needs identical atom counts?

Hi, I am using color_by_mutations on PyMol 1.3. http://www.pymolwiki.org/index.php/Color_By_Mutations I get this error: PyMOLrun color_by_mutation.py PyMOLcolor_by_mutation aav2, aav8 ExecutiveRMS-Error: Atom counts between selections don't match (30882 vs 30227) Executive: Error -- no atoms

[PyMOL] superimposing pse files

Hello everyone, I have created molecular tunnels for two starting points using CAVER and saved them as two different pse(Pymol session) files. Is there any way I can superimpose the two tunnels? Can I superimpose the two pse files (I tried and it doesn't happen. One pse overrides the other). I

Re: [PyMOL] fink install pymol help

On Mar 15, 2012, at 10:14 PM, Shane Neeley wrote: I've installed all of the packages for pymol-py27 with fink. And my terminal went back to normal. Now what? How do I make PyMol an application? Short answer: You don't. The fink version of PyMOL is run from the command line. Open up a new

Re: [PyMOL] superimposing pse files

Hi Sajeewa, load sessionA.pse load sessionB.pse, partial=1 This will essentially merge sessionA and sessionB. Make sure sessionA and sessionB do not have objects with the same names--it'll just confuse PyMOL if they do. To transform the mesh/surfaces after aligning the proteins see the

Re: [PyMOL] superimposing pse files

Sajeewa, 1) Is there a way of changing the object names in a session file so that pymol will not get confused when I merge two sessions having  objects with the same name? You need to ensure that each session has file names that will not collide with name in other sessions. Rename each object