[Chimera-users] Chimera morph colors with morph conformations

[Ahmad Khalifa]

Thank you so much, is there a way to set the frame speed with coordset?

On Wed, Sep 26, 2018 at 12:59 PM 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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