[Chimera-users] Chimera morph colors with morph conformations

[Elaine Meng]

Correction to my previous answer:  it is possible to morph colors at the same time as playing the morph trajectory using a command script.

For example, if I have scene named “1” which is frame 21 of the morph trajectory in one color, and another scene named “2” which is frame 41 of the morph trajectory in another color, then the following command plays from 21 to 41 while morphing the color at the same time:

scene 1 reset; coordset #2 21,41; scene 2 reset 20; wait 20

As to whether morphing the colors at the same time as playing the trajectory is the best way to show what you want, it depends on artistic or personal preferences, so I’ll leave it up to you to decide!

Best,
Elaine


> On Sep 26, 2018, at 9:59 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hello Ahmad,
> To answer your previous question, you can play back the morph trajectory (or other trajectories) with the “coordset” command.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
> 
> My approach to making movies with morphs in them is to use command scripts.  Here are two examples of such movies that you can play, and links to their Chimera command scripts:
> 
> (1) Morphing between the inactive and activated conformations of the FGFR1 kinase domain.
> <http://www.rbvi.ucsf.edu/chimera/animations/animations.html#kinase-morph>
> 
> (2) Ball-and-socket motion.
> <http://www.rbvi.ucsf.edu/chimera/animations/animations.html#trmovie>
> 
> However, I haven’t made a movie where I morph the color at the same time as playing the morph trajectory.  According to my testing just now, it cannot be done in commands.  Instead you have to use the Animations dialog.  You would have to show one step (the starting point) of the trajectory with one color, save a scene, then show the endpoint step, change color, and then save a second scene.  Then you have to move both scenes down to the timeline and play (and record if you want).  There could be other scenes on the timeline that are not different steps in morphing, with other changes in display, coloring, labels, etc.
> 
> You can use “scene” command to save and restore scenes in a command script, but I could not find any way that would gradually change the color at the same time as playing the morph with “coordset.”
> 
> I personally prefer to use command scripts rather than saving a giant session with all the scenes in the timeline. However, the timeline and graphical Animation tool may be easier to use if you are not experienced with commands.  You would still have to spend some time learning how to use the Animation tool.  Here is its help page:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/animation/frameanimation.html>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Sep 26, 2018, at 7:34 AM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
>> 
>> Hello,
>> 
>> I'm trying to create a movie with morph conformations. I wonder if it's possible to morph the colors, or change colors midway through, going from one conformation into the other.
>> 
>> Please feel free to contribute any ideas or thoughts on how to make my movie  clearer and more visually aesthetic. 
>> 
>> Thanks. 
> 
> 
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