Hi Donna, I don't know specifically what parameters might help but you can see in the help page which options are available with this command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#morph-parameter...> Did you try using the defaults first to see what you get? Usually the corkscrew method is better than linear, and your minHingeSpacing seems quite large. Every system is different, however. In the ones I've worked on, the defaults are usually reasonable but I've occasionally adjusted the coreFraction, or had to resort to manually building an intermediate state. The latter is a pain and I don't have an easy recipe for that. You would (using whatever approach you can think of) manually generate an in-between conformation and then do a 2-stage morph between the original start structure and your intermediate, then from the intermediate to the original end structure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Jan 27, 2026, at 3:14 AM, Matzov Donna via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I'm trying to morph two conformations of the same protein in which one of the helices moves while it rotates. I used the following command:

#morph #1,2 frames 101 wrap t method linear minHingeSpacing 20

While moving from one state to the other, the helix mentioned above is distorted (it starts and end looking good but in the middle it loses it's helical shape).

Could I add/change on of the parameters to fix that?

Many thanks,

Donna Matzov, PhD Department of Structural Biology Weizmann Institute of Science The Shalev-Benami Lab