Assistance with ChimeraX Syntax for SPRITE Hands-On Module
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
Hi Zeenat, I see on page 10 of the PDF you attached that you align using Chimera command match #0:57.c,102.e,195.f #1:157.a,102.a,195.a In ChimeraX the command would be align #1/C:57 #1/E:102 #1/F:195 to #2/A:157,102,195 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. Here is the documentation for the ChimeraX align command. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/align.html It is the same as the Chimera match command. Tom
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 <mailto:bashirz@seas.upenn.edu><01 SPRITE Chimera Student Module.docx>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
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Tom Goddard -
Zeenat Bashir