- ChimeraX-users - RBVI Mailing Lists

Permission denied to "Spin Movie"
by Pam Cook 17 Apr '23

17 Apr '23

Hi, I just installed ChimeraX on macOS Catalina 10.15.7. During installation, it asked me to allow access to desktop files and I said NO. But now, when I try to create a SpinMovie file, I get the message: Permission denied reading directory "/Users/pam/Desktop" while trying to determine next unused file name movie#.mp4. I guess I should have said YES to the question above. How can I fix this? Thanks, Pam

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Question about using ChimeraX
by 韩磊 17 Apr '23

17 Apr '23

Dear Sir， I hope this mail finds you well. I am a professional researcher from Tianjin Medical University, China. I have encountered some difficulties in learning to use ChimeraX software. First, I would like to know if the software can be used to construct a graph of the process of channeling proteins from closed to open state (e.g., Appendix ). Second, we can currently only download and import a model of the closed state of a protein into the software, but it does not reflect its conformational changes, so I would like to know which option within the software can change the conformation of the protein. Sincerely yours, Lei Han, Ph.D. Tianjin Neurological Institute, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin 300052, China

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Could you please inform the best advice to solve a structure via colabfold when GPU is an issue? I tried some routes already.
by Josh Gutierrez 14 Apr '23

14 Apr '23

Hello, I recently submitted a job through ChimeriaX and used the "prediction" task for it to be solved via Alphafold2-- the sequence is about 1300 amino acids in length. However, the protein could not be solved by alphafold2 and the colabfold reports the GPU consumption is too high for the structure to be solved. To resolve the problem, I tried breaking the sequence into two to solve this expected bimodal protein individually (into two separate structural parts) and even in combination purchased "compute units" for more memory and storage to do this, but the structure can't be solved without high predicted error. Please let me know what you think may resolve this issue. Currently, I am working with an external professor who may be able to connect me with a collaborator on this issue at UCSF if there is a cluster or core we can use to expedite the process to solve this structure I am addressing. Please let me know your thoughts at your earliest convenience. Please also let me know if you need any more information! Many thanks, Josh Gutierrez

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Measure inertia and measure center on aligned density maps and models
by Kevin Felt 13 Apr '23

13 Apr '23

Dear developers, I am trying to compare the center of mass of multiple cryo-EM maps and models. The receptor is the same in all cases, just the ligand bound in the binding pocket varies. I want to show a directionality to how the ligands are binding in the pocket between the structures, so I have aligned the maps and models together and am attempting to run "measure center" and "measure inertia" to initiate this comparison. However, when I run these commands, the output markers and ellipsoids are not positioned in an aligned fashion as their parent objects, but rather in there initial positions before alignment, which is not useful for comparisons of the subtle movements between structures. Additionally, if I could get the measurements to work on the aligned structures, is there a tool in ChimeraX that would allow me to draw vectors from a reference point to the center of masses? Furthermore, is center of mass the correct parameter for comparison of densities that are variable in shape? (e.g. comparing the relative position of a long and flat density to a short a globular density?) Thank you! Sincerely, -- Kevin C. Felt PhD Candidate - Chakrapani Lab Department of Physiology and Biophysics School of Medicine Case Western Reserve University

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Modeling post-translational modifications
by Guillaume Gaullier 13 Apr '23

13 Apr '23

Hello chimerax-users, I am trying to model a PTM, and the most sensible way to me seems to use the swapaa command and specify the sensible monomer from the PDB Chemical Component Dictionary as the target residue. Here is what I tried (residue #1/a:9 is a Lys): open 1kx5 swapaa #1/a:9 KCX And the error I got: Dynameomics rotamer library does not support KCX I tried all the rotamer libraries listed in the swapaa help page ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/swapaa.html#rotLib ), but none of them can provide stereochemical info for KCX. I can open the monomer I want (carbamylated Lys) with: open ccd:KCX But of course in this case it’s floating by itself as a new model, not incorporated in the protein sequence and structure I am interested in. Is this the correct way to model a PTM? If it is, where can I find a rotamer library that will contain the stereochemical info for KCX, and how do I tell ChimeraX to use it? If it is not how modelling a PTM is done, then how else should I do this? Thank you in advance, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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unifold
by Roger Leng 12 Apr '23

12 Apr '23

Dear Administrators, Is it possible to add "unifold" in your prediction, just like Alphafold? Thank you. Sincerely, Roger Leng

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Problem Installing ChimeraX
by Stephen P. Molnar 12 Apr '23

12 Apr '23

I am running an up-to-date installation of Debian Bullseye on my Linux platform. My attempt to install ucsf-chimerax_1.5ubuntu20.04_amd64.deb generated an interesting error message: sudo apt install ucsf-chimerax_1.5ubuntu20.04_amd64.deb [sudo] password for comp: Reading package lists... Done Building dependency tree... Done Reading state information... Done E: Unable to locate package ucsf-chimerax_1.5ubuntu20.04_amd64.deb I have managed to install Chimera, both Linux and Windows versions, many times without any problems. Guidance would be much appreciated. Thanks in advance, -- Stephen P. Molnar, Ph.D. https://insilicochemistry.net (614)312-7528 (c) Skype: smolnar1

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ChimeraX Python Shell Errors
by Aashna Soni 10 Apr '23

10 Apr '23

Hi, I hope this email finds you well. I am trying to use the ChimeraX Python shell to run commands programmatically (such as opening different protein structures, extracting the number of hydrogen bonds from a structure, changing the sel number, and saving the log file). When I try to run this command: run(session, "open <insert filepath>"), I am getting this error: "AttributeError: module 'chimerax.core.session' has no attribute 'ui'." I am getting similar errors when I run any run(session, ...) command, such as the first one on this tutorial: https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/introduction.html. These commands were working around a month ago, and I am not sure why they are not working now. Could you please help me resolve this issue? Thanks in advance. Warm regards, Aashna

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Re: [chimerax-users] [Chimera-users] Chimera cannot read multi-molecules .xyz files in
by Elaine Meng 07 Apr '23

07 Apr '23

Hi Francois, I'm told that although ChimeraX itself does not read XYZ files, you can add that capability by installing the SeqCrow plugin. ChimeraX menu: Tools... More Tools wil show the Toolshed website in the ChimeraX browser, in which you can find SeqCrow and install if it you like. Here is the URL where you can see information about SeqCrow, but to install, it is more convenient to use the ChimeraX menu and browser as mentioned above. <https://cxtoolshed.rbvi.ucsf.edu/apps/seqcrow> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 6, 2023, at 9:40 PM, Francois Berenger via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Apparently, chimerax cannot even open a single-molecule .xyz file ?! > > ---------- Forwarded message --------- > From: Francois Berenger <berenger(a)edu.k.u-tokyo.ac.jp> > Date: Fri, Apr 7, 2023 at 1:09 PM > Subject: Chimera cannot read multi-molecules .xyz files in > To: <chimera-users(a)cgl.ucsf.edu> > > > Dear list, > > I can read one molecule fine in .xyz format using chimera. > > However, if my .xyz file has several molecules (like a MD trajectory), > chimera fails to read it in. > > Is there planned support for MD trajectories given as .xyz file? > > I have chimera-1.16. > I shall test with ChimeraX very soon. > > Regards, > F. > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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REQUEST: Vendor Voluntary Product Accessibility Template (VPAT) or Accessibility Conformance Report (ACR) - UCSF Chimerax Software
by Powers, Gina 07 Apr '23

07 Apr '23

Good Morning, I am requesting a copy of the Vendor Voluntary Product Accessibility Template (VPAT) or Accessibility Conformance Report (ACR) for review regarding UCSF Chimerax Software for a user. Gina Powers | Program Analyst Division of Regulatory Science Informatics | CTP-OS | FDA Accelerate the transition to a healthier America Office: (240) 402-3188 Email: Gina.Powers(a)fda.hhs.gov<mailto:Gina.Powers@fda.hhs.gov> CSC Email: CTP-OS-CSC(a)fda.hhs.gov<mailto:CTP-OS-CSC@fda.hhs.gov> Have a CSC question? Feel free to send it to OSCAR<https://oscar.fda.gov/> - the 24/7 CSC chatbot! [cid:image004.png@01D96936.F819C850][cid:image003.png@01D96936.F30B6120] Division of Regulatory Science Informatics

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