[Chimera-users] Morph Help

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 25 12:59:48 PST 2019

Hi Debamita (Paul),
You may not always be able to get the trajectory you want.  All I can suggest is  to try:

(1) changing morph parameters.  You did not say whether you were using Chimera or ChimeraX.  Both allow changing method and core fraction, or forcing Cartesian intermediates (the latter has not been useful in the cases I’ve worked on, however).  ChimeraX also allows changing hinge spacing.

(1b) Chimera has an option to minimize each frame, but it also has limited ability to “rescue” bad conformations, and it will take a lot longer to calculate your morph trajectory.

(2) more difficult, if (1) does not solve your problem:  manually create intermediate states to “guide” the overall trajectory and then morph in more stages involving these intermediates.  I.e instead of morphing 1->2, create 1a and possibly 1b etc. then morph 1->1a->1b->2.

I hope this helps.

For future reference, to make it more likely you get your questions answered, please send to chimera-users at cgl.ucsf.edu or chimerax-users at cgl.ucsf.edu (depending on which program you’re asking about).  Thanks,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 25, 2019, at 12:30 PM, Paul, Debamita <Debamita_Paul at baylor.edu> wrote:
> Hi,
> I am trying to morph two structures having a DNA lesion (6-4 Photoproduct). However the movie is showing weird geometry in the intermediate steps. Is there a way I can provide the parameter file for the 6-4 so that the geometry is not messed up.
> Thanks
> Debamita

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