[Chimera-users] Query on morph command in Chimera

Mario J. Borgnia mborgnia at helix.nih.gov
Sun Mar 22 14:05:56 PDT 2015


Vinoth,

I forgot to mention that this command pair (separated by ;):

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

behaves differently from:

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

In the latter, "step" refers to the binning of the data of the morphed
volume, which is done somewhere before the morph is displayed. This
issue is especially confusing for large volumes because the decision
regarding the step that will be used to display the data (the actual
step and not the binning) is done based on the size of the volume. Thus,
if you start with a volume that is large, Chimera will increase the step
and display the data as if binned, indicating the value of the binning
as a "step" in the "volume viewer". Thus, using "step 1" in the vop
command will not bin the morph map and the display will stay at step 4.
If, instead, you were to use:

vop morph #0,2 constantVolume True model #3 frames 200 step 4

The result will look the same, but now the actual data of the morph will
be binned by 4 and the "step box" on "volume viewer" will read "1". Now
if you notice the size of the volume indicated next to the name, it will
be binned. (e.g. 60^3 instead of 240^3).

I hope this helps understand what's going on.


Mario




On 03/22/2015 04:36 PM, Mario J. Borgnia wrote:
> 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
>
>
> Best,
>
> Mario
>
>
>
> 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
>>
>>
>>
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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| Mario J. Borgnia, Ph. D.        |
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| Lab of Cell Biology             |
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