[chimerax-users] morph with molecular surface for part of molecule

[Elaine Meng]

Hi Susan,
Unfortunately it’s not as friendly as Chimera (yet).  You would need to force recomputing the surface at each trajectory frame, for example with commands like the following for morph trajectory model #3:

alias stuff surf close; surf #3 & protein
perframe stuff; coordset #3 1,21; wait 21; ~perframe

In that example I first create an alias “stuff” (could be some other word) that includes all the actions I want to do at each frame, then define it as a per-frame action to occur at each step of trajectory playback with the “coordset” command.  The “wait” is required so that stopping the perframe action with “~perframe” won’t happen until after all the trajectory frames are played.

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/wait.html>

Closing the surface is also required because otherwise “surface” thinks it doesn’t need to do anything because a surface for the same set of atoms is already there… it isn’t smart enough (yet) to realize that the atoms may have moved around.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 29, 2019, at 8:52 AM, Susan Lea <susan.lea at path.ox.ac.uk> wrote:
> 
> How can I generate a morph with a molecular surface representation?
> 
> many thanks
> Susan
> 
> Prof. Susan M. Lea,  FMedSci                      tel: +44 1865 275181
> ------------------------------------------------------------------------------------------
> Director of the Central Oxford Structural Microscopy and Imaging Centre & Professor of Microbiology
> Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ WadhamCollege
> 
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