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  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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