February 2023 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] Help getting rmsd value per residue of 2 similar structures.
by Elaine Meng 08 Feb '23

08 Feb '23

Hi Binh, This is almost the same question as asked yesterday on chimerax-users(a)cgl.ucsf.edu, so I have the same answer: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004923.html> That answer assumes you are using Matchmaker to superimpose these structures first, which has an option to display the pairwise sequence alignment with RMSD values per column, which can then be written out, used for coloring, etc, as detailed in that answer. Note that this RMSD is only using CA atoms so for two structures, it is simply the distance between the 2 CA atoms. You can use the Sequence Viewer settings to make it use the 4 backbone atoms per residue instead (N,CA,C,O): <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004923.html> Secondarily, remember that Chimera and ChimeraX are two different programs and if you are viewing help/answers for Chimera they may not pertain to ChimeraX. Finally, for the best chance of getting a good answer to ChimeraX questions in the future, please use chimerax-users(a)cgl.ucsf.edu unless you are including private data. Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 8, 2023, at 12:39 PM, Binh Nguyen <AnBinh.Nguyen(a)UTSouthwestern.edu> wrote: > > Dear Elaine, > > Is there a way to generate the rmsd per residue of 2 similar structures using chimeraX? I have searched through but I can only manage to get the overall RMSD. > > I have found this too but I have no idea how to get such information. > https://www.rbvi.ucsf.edu/pipermail/chimera-users/2019-February/015415.html > > Please help, thank you. > > B

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Questions about MultiAlign Viewer
by Beate Aftret 06 Feb '23

06 Feb '23

Hi, I have some issues accessing the Multiaglin Viewer in ChimeraX. I’ve tried to look at this response: https://www.rbvi.ucsf.edu/pipermail/chimera-users/2019-February/015415.html . However, I’m unable to access it. I’m trying to access the multialign viewer so I can get individual RMSD values on structures compared using Matchmaker. Thank you in advance. Let me know if I need to give more detail. Kind regards, Beate Aftret

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No Access to Personal Files
by Anna Popa 02 Feb '23

02 Feb '23

Good afternoon, I am a college student using your ChimeraX software to complete an assignment in my biochemistry course. I have downloaded your app to my HP Chromebook using the most recent Ubutun version. Despite being on my personal computer, ChimeraX cannot open the files needed from my computer. When I tried to find out why this is happening, I concluded that it might be a software issue because I wasn't even able to set up the ChimeraX app completely. I would greatly appreciate some guidance and assistance. Thank you, Anna Popa

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Fwd: Your message to ChimeraX-users awaits moderator approval
by Eric Pettersen 02 Feb '23

02 Feb '23

> Begin forwarded message: > > From: Krishnan Raman > Subject: RE: Your message to ChimeraX-users awaits moderator approval > Date: February 2, 2023 at 9:47:12 AM PST > To: "chimerax-users-owner(a)cgl.ucsf.edu" <chimerax-users-owner(a)cgl.ucsf.edu> > > Hi guys > > is there a way to get structures + other numerical data into chimerax? > I get the structures using a sdf file. I want to get in someother data associated each structure. > > How to start multiple instances of chimerax from a html-commands file? > Thanks > Krish > 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. >

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Obtain electrostatic potential from PQR/DX via script
by Lohry, David 02 Feb '23

02 Feb '23

Hi everyone, I'm performing an analysis where I want to select different regions on a molecule and obtain a list of all of the electrostatic potentials from that region. My input is a PQR file with a DX file. These were generated from a PDB and APBS. The electrostatic potential can be viewed when the option "Report value at mouse position" is selected in the Surface Color tool (Tools...Volume Data...Surface Color...Options button) In the status bar at the bottom, it will show the value along with the coordinates. Is there a way to obtain this information via a ChimeraX command that I could script? Thank you!

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ChimeraX-users February 2023