A few things to notice. In ChimeraX the model numbers start at 1 whereas in Chimera they start at 0. In ChimeraX a chain is specified with the slash character "/", for instance /A:57 for residue 57 of chain A while in Chimera the notation is :57.A. And in ChimeraX you cannot use #1/C:57,/E:102 where you omit the #1 for the chain E residue because the comma after the 57 only allows specifying more residues as in #2/A:157,102,195. So it is necessary to say #1/C:57 #1/E:102 repeating the "#1" part. In the ChimeraX command the word "to" appears between the two sets of residues given in the command.

On Feb 18, 2025, at 6:41 AM, Zeenat Bashir via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX Developers,

I hope this email finds you well! I am currently developing a hands-on module for my students on visualizing SPRITE results using ChimeraX. However, I am facing an issue with the syntax for aligning the residues of 2HNT with 1A0J. The module I am using, which was provided by Basil (attached with this email), includes syntax for Chimera (refer to Figures 10 and 11 in the attached document). I have tried adapting the syntax for ChimeraX but have not been successful. I would really appreciate your guidance on this matter or if you could direct me to someone who might be able to assist in generating the correct command line syntax.
Thank you so much for your time and help!
Zeenat
--
Dr. Zeenat Bashir
Senior Lecturer
Biotechnology Lab Coordinator
Department of Chemical and Biomolecular Engineering
University of Pennsylvania
310 Towne Building
220 S. 33rd Street
Philadelphia, 19104 -6393
bashirz@seas.upenn.edu
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