Hi, How do I use swapaa to do mutations on seven to ten residues in one command? Thanks Krish Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.
Hi Krish, You can only do that if they are all changing to the same type. With that caveat, simply specify all the residues in that one command, e.g. swapaa /A:12-14/B:8,13 arg ...would change residues 12-24 in chain A and residues 8,13 in chain B to arginine. See "swapaa" usage as well as general page on command-line specification of atoms, residues, etc. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/swapaa.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 22, 2023, at 1:19 PM, Krishnan Raman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, How do I use swapaa to do mutations on seven to ten residues in one command? Thanks Krish
Hi Elaine, Thanks. Let me try to play with that a little more. Always appreciate your quick response and help. Krish -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Sunday, July 23, 2023 12:45 PM To: Krishnan Raman <RKrishnan@BIOCRYST.com> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Swapaa doubt [EXTERNAL] Hi Krish, You can only do that if they are all changing to the same type. With that caveat, simply specify all the residues in that one command, e.g. swapaa /A:12-14/B:8,13 arg ...would change residues 12-24 in chain A and residues 8,13 in chain B to arginine. See "swapaa" usage as well as general page on command-line specification of atoms, residues, etc. <https://link.edgepilot.com/s/c460dc4f/DLMHg87i0EmgGzeT6eODtA?u=https://rbvi.ucsf.edu/chimerax/docs/user/commands/swapaa.html> <https://link.edgepilot.com/s/8f52e1b2/Y-AN5a7sXkOiO2YkvPWiZw?u=https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 22, 2023, at 1:19 PM, Krishnan Raman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, How do I use swapaa to do mutations on seven to ten residues in one command? Thanks Krish
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