And is there a way to display the ion coordination pseudo-bonds all the way through the interpolation? Now they are only displayed (even only seem to exist?) on the first frame, and the coordset documentation doesn't mention this (I read more carefully this time...). If not I will simply hide the pseudo-bonds. Thank you, Guillaume ________________________________ From: Guillaume Gaullier Sent: Thursday, October 1, 2026 9:57:42 AM To: ChimeraX Users Help Subject: Re: [chimerax-users] morph command ignores ions in metalloproteins? Once more I skimmed the documentation too fast... thank you! đ ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, September 30, 2026 5:37:55 PM To: Guillaume Gaullier Cc: ChimeraX Users Help Subject: Re: [chimerax-users] morph command ignores ions in metalloproteins? Hi Guillame, It's covered in the "atoms in common" section of the morph documentation. Namely, you need to use "same true": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> The zinc is in the morph when I have these structures open as #1 and #2 and use command morph #1,2 same true 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 Sep 30, 2026, at 2:23âŻAM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I am trying to make a morph between PDB entries 9SKS and 9SKT. The protein does what I want, but I can't find out how to include the active site :ZN in the interpolation. This ion is consistently numbered between both structures, and I give model numbers to the morph command, which should select the entire models including their ions. Nothing about this in the documentation. What am I missing?
If interpolating ions with morph is impossible to do for some reason, then it would be helpful to list it in the "limitations" section of the command's documentation.
Thank you in advance,
Guillaume
--- Guillaume Gaullier, PhD Researcher, Blikstad group Molecular Biomimetics / Microbial Chemistry Department of Chemistry - à ngström Uppsala University RegementsvÀgen 10 752 37 Uppsala Sweden
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