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 obje

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 matrix_co

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 Term

[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 wan

[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: PyMOL>run color_by_mutation.py PyMOL>color_by_mutation aav2, aav8 ExecutiveRMS-Error: Atom counts between selections don't match (30882 vs 30227) Executive: Error -- no atoms

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 wrote: > Dear PyMOL List > What is the segi-identifier? > > Thanks fo

[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] 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 h

Re: [PyMOL] loop through pymol models

And: print models print len(models) print models[0] /Troels 2012/3/16 Troels Emtekær Linnet > models=cmd.get_names() > > python > for model in models: > print model > python end > > /Troels > > > 2012/3/16 Matthias Schmidt > >> Hi, >> >> I would like to have a python script that runs in pymo

[PyMOL] loop through pymol models

Hi, I would like to have a python script that runs in pymol and loops through all available loaded models. How do I get the number of models loaded in pymol? Thanks, Matthias -- This SF email is sponsosred by: Try Windo