[Chimera-users] help

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 30 09:52:22 PDT 2013


Hi Sreekanth,
Morphing makes a trajectory that is shown by the MD Movie tool.  You can save loaded trajectories to PDB using the main Chimera menu "File... Save PDB"

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

In the resulting dialog, choose just the morph model (not the other models input to morphing) and then indicate whether you want to save only the "current frame" or "all frames."  If all frames you will get a multi-model single PDB file, like what is used for NMR ensembles in the Protein Data Bank.

The trajectory is also saved in a Chimera session file and could be played back with the command "coordset"
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
(see also the "ball-and-socket motion" movie and command script in the Chimera Animation Gallery <http://www.rbvi.ucsf.edu/chimera/animations/animations.html>)

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. a more useful e-mail subject line might be "saving a morph" instead of "help" :-)

On Aug 29, 2013, at 6:41 PM, rajan sreekanth wrote:

> Hi,
> I had morphed two conformations (open and close) of my protein using 'Morph Conformations' tool. I want know whether we can save the coordinates capturing the intermediate states? Something like an NMR ensemble consisting of the open-intermediate states-close conformations as a single PDB file?
> Thanks 
> Sreekanth 




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