[Chimera-users] Query on morph command in Chimera

Mario J. Borgnia mborgnia at helix.nih.gov
Sun Mar 22 13:36:32 PDT 2015

Hi Vinoth and Elaine,
I stumbled upon the same problem. I think Vinoth is referring to "step"
rather than "level". If that is the case, the following command would do
the trick:

vop morph #0,1,2 constantVolume True model #3 frames 200; volume #3 step 1



On 03/22/2015 12:57 PM, Elaine Meng wrote:
> 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
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
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| Mario J. Borgnia, Ph. D.        |
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