[Chimera-users] Chimera morph map multiple volumes

Elaine Meng meng at cgl.ucsf.edu
Sun Nov 15 17:16:25 PST 2020

Hi Ahmad,
Example of "bouncing":  If you use playStep 0.1 then it would take 10 frames to go from one map to another (0.0 to 1.0): in other words, the number of frames needed for playRange is 1.0 divided by the playStep value.  Then, if you specify 20 frames (keeping playStep 0.1), it will play forward from 0.0 to 1.0 and then bounce backwards from 1.0 to 0.0.  That is the answer of how you play back and forth.

Or, you could have two "vop morph" commands with option "playDirection 1" (for the forward play) and "playDirection -1" (for the backward play).


To record you would have a Chimera command script with "movie record" before the morph playback with "vop morph", followed by "movie stop" and "movie encode."


There is no option to show the GUI for playback, sorry.

The reason you get 1->0 ->2 ->6 ->2 ->0 ->1 when you specify #1,0,2,6,0,1 is that you cannot give the same model number twice.  When you specify #1,0,2,6,0,1 it sees that you have specified four maps, #1,0,2,6.  Maybe you can make copies of #0 and #1 using "vop copy" and then specify the copies in the command so that the same number is not repeated.

The "vop morph" command includes a "step" option. Click the "new-map-options" in the "vop morph" help (the first link above) and it will list those options.

Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 15, 2020, at 3:12 PM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> Hi Elaine,
> I think I get what that means, however, how can I calculate the number of frames needed for the entire playRange? 
> The other thing that I'm rather confused about is that when I run the following command: 
> vop morph #1,0,2,6,0,1 playStep 0.1 hideOriginalMaps true interpolateColors true frames 500 modelID #3
> I get a morph that would correspond to 1->0 ->2 ->6 ->2 ->0 ->1!!! Why is it showing 2 a second time?! I tried to restart chimera but the issue remains!
> P.s. is there a way to set the "volume viewer step" for the morph, so I don't have to set it manually in the viewer and then supply the modelID such as what's above?
> Thank you so much. 
> On Sun, Nov 15, 2020 at 12:26 PM Ahmad Khalifa <underoath006 at gmail.com> wrote:
> Thanks a lot Elaine. The command line seems to work, but the gui does have nice features! This part is rather confusing 
> " If the number of frames and step increment are more than needed to reach the playRange bounds (default is the entire range: 0.0,1.0), the morph display will “bounce” back and forth."
> So I wonder how to play the morph back and forth similar to the gui, and actually, how to only play the morph in a single direction, but from the gui. I also wonder if there's a quick record option similar to the gui, or do I have to use movie encode? It would also help if I can find the log of how all these gui commands are passed to chimera so I can customize it and use it for  the command line interface. 
> Cheers. 
> On Sun, Nov 15, 2020 at 9:46 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Ahmad,
> To morph between multiple maps (more than two) you have to use the command "vop morph" instead of the Morph Map tool.  For example,
> vop morph #1,2,5
> ... but there are a lot of additional command-line options that you may want to use, see:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#morph>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Nov 14, 2020, at 9:06 PM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> > 
> > Is there a way to morph multiple volumes into a single movie? I tried morphing two maps first with the hope that I can do another morph between the resulting morph and a third map, but it didn't work. Any suggestions or easy alternatives to join the morphs together?
> > 
> > Thanks.  
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