[Chimera-users] Query on morph command in Chimera

[Elaine Meng]

On Mar 22, 2015, at 9:38 AM, vinothkumar <vkumar at mrc-lmb.cam.ac.uk> wrote:

> Dear Elaine,
> I have three different volumes/maps of the same protein but differing in conformation. I am able to use the command line - ‘vop morph #0,1,2 constantVolume True model #3 frames 200’ which then interpolates and I could produce a movie. However, by default the threshold for the volumes and level goes to 4. Is there a way to insert in the command line to tell that all the volumes be set to level (1) and a certain threshold.
> Thank you
> Regards
> Vinoth

Dear Vinoth,
You should adjust the threshold of the maps before the morphing.  This could be done with the “volume” command if you are not using GUIs, e.g. command:

volume all level 1

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>

Actually, my own experiments suggest it is only the threshold of the first input map that matters in setting the starting level of the morph.  If you use the “constantVolume” morphing option, however, the threshold will be adjusted to keep the enclosed volume constant.  If you really wanted to keep it exactly at 1 through the whole morph, you would not use that option.

I hope this helps! For future questions, we recommend you send them to chimera-users at cgl.ucsf.edu (CC’d here) instead of to me or other individuals directly, unless you are including private data.  Thanks,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco