[Chimera-users] Drawing vectors depicting the movement of one conformer to another

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 12 09:02:57 PST 2018

Hi Beth, 
Well, it would definitely be a project and would take some time to investigate and decide whether it is even possible to achive the look that you want.  In principle, each of the things can be done.  

Besides rigid-body rotation and translation (and saving positions, see commands “savepos" and “reset"), there is also morphing from one conformation to another (Morph Conformation tool or “morph” command).  However, depending on your input structures, you might have to make some intermediate structures by hand and do the morphing in multiple stages to get the overall change to look how you how want it to.  There are also various parameters that can be tweaked in morphing. I’ve done a multi-stage morphing of proteins for a movie, including creating intermediates by hand, and it took several days to get all of this just right.  Should also say I haven’t tried morphing RNA.   Most recently I’ve used ChimeraX instead of Chimera because it has essentially all of the movie-related commands (although some are different commands or syntax than in Chimera) and the “morph” command is easier to use, but the disadvantage relative to Chimera is that the session format is not yet stable.

First you would try morphing to see if it gives what you want, and if so, you would just create the morph trajectory or trajectories (if multi-stage) once and then save a session.  Then when scripting/recording the movie, you don’t recalculate the morph, you only judiciously hide the other model numbers and only show the morph trajectory model while playing it back with the “coordset” command.  For examples including Chimera command scripts, see the Animation Gallery top entry (kinase morph) and about halfway down the page, “ball-and-socket motion” 

See also making movies, movie-related commands

The vectors might be difficult.  You can create 3D arrows in the BILD forrmat (simple text format) and read them in and include them in your saved session, but the hard part is calculating where they should be (endpoint coordinates) or just positioning them by hand and eye.

Another possibility might be just to add pseudobonds between atom starting and ending positions assuming they are in two different structures both open in the session (e.g. by creating a list of atom pairs and reading it in with PseudoBond Reader) but that would just give lines, not arrows.

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

> On Nov 12, 2018, at 5:22 AM, Beth Stroupe <mestroupe at bio.fsu.edu> wrote:
> Hi,
> I would like to make a figure depicting the movement of an RNA molecule from one conformation to another. It is not a simple rigid body rotation or translation but a rolling motion where some parts of the molecule move more than others. I would like to show vectors to show the rotation that are colored coded by the distance of the move.
> Is there a straightforward way to do this in Chimera?
> Thank you,
> Beth

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