Re: [PyMOL] Saving trajectory outputs

[Thomas Holder]

Hi James,

you can save multi-model PDBs with state=0:
PyMOL save trajectory.pdb, state=0

There is also a save_traj function in PSICO which can write DCD format:
http://pymolwiki.org/index.php/Psico

The latter is based on the save2traj script by Sean Law:
http://pymolwiki.org/index.php/Save2traj

Cheers,
  Thomas

On 25 Jul 2014, at 04:24, James Starlight jmsstarli...@gmail.com wrote:

 Dear Pymol Users!
 
 I wounder whether it will be possible  to save big ensemble of the loaded 
 into pymol Pdb's files as the trajectory output (like dcd format) what are 
 actually can be performed by vmd (e.g by means of 
 http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/). The 
 problem in last case is that I don't know how to perform superimposition of 
 my conformers agains refeence frame (alternatively what is easily performed 
 in pymol). I'll be thankful for any suggestions.
 
 Best wishes,
 
 James

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


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[PyMOL] Saving trajectory outputs

[James Starlight]

Dear Pymol Users!

I wounder whether it will be possible  to save big ensemble of the loaded
into pymol Pdb's files as the trajectory output (like dcd format) what are
actually can be performed by vmd (e.g by means of
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/).
The problem in last case is that I don't know how to perform
superimposition of my conformers agains refeence frame (alternatively what
is easily performed in pymol). I'll be thankful for any suggestions.

Best wishes,

James
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