[Chimera-users] Animating peptide bond formation

Elaine Meng meng at cgl.ucsf.edu
Sat Aug 11 12:02:13 PDT 2018

Dear Alex,
The software isn’t really intended for showing chemical reactions (changes in bonding) so you’d have to do something kind of simple, for example:

Say you had 3 models, the two parts not bonded to each other and the third model being the whole structure with the bond.  You could move the two parts farther apart initially and save that as one position (see savepos/reset commands) then gradually move them to another previously saved position that is exactly superimposed with the corresponding parts of the bonded structure, but with that third model hidden.  Then crossfade to view with the two parts hidden and the third model shown.  See “movie crossfade” command. 

If you wanted to do something fancier like showing the change in nitrogen hybridization as the bond is formed, that would definitely be more work, and I haven’t figured out how exactly it could be done (or even if it’s feasible with a reasonable amount of work).

See movie-related commands list for details on the commands:

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

> On Aug 11, 2018, at 11:45 AM, Alex Nazlidis <nazlidisalex at gmail.com> wrote:
> Dear Chimera users and staff,
> I've been thinking of ways to animate the formation of a peptide bond between two aminoacids but I haven't come up with a solution. Can you help me out here? :) 
> Thanks in advance, 
> Alex Nazlidis

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