April 2023 - ChimeraX-users - RBVI Mailing Lists

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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Multichain comparative modelling
by Prof. Dr. Kay-Eberhard Gottschalk 06 Apr '23

06 Apr '23

Hi There, I am interested in a complex formed by a protein with two domains connected by a long loop in complex with a second Protein, that binds this loop, causing it to form a short helix. I have two pdb stuctures: One with the two domains in the correct relative domain orientation, connected by an unstructured loop, and one with the part of the loop forming a helix in complex with a second Protein. I am sure that comparative modelling can do the trick, but somehow I dont understand the workflow. Do I need do load both templates into chimeraX, oben sequence file conatining both Proteins and load that also, if so in which format? I went over the Manual, but somehow it is not clear to me. Thanks a lot for your help! Best, Kay

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About displaying electron density maps (MTZ format) in chimerax
by Laurent 05 Apr '23

05 Apr '23

Hi, I am currently trying to display an electron density map (from a MTZ file) in ChimeraX, but it seems that the display box size is limited. I would like to display the maps around ligands in an oligomeric protein, where the ligands are quite far from each other. Is there any way to increase the box size of the displayed map so that it covers all ligands ? Thanks ! Laurent Laurent Maveyraud Professor of Biophysics | University of Toulouse | Structural Biophysics Team Doctoral School Biology - Health - Biotechnologies +33 5 61 17 54 35 | +33 6 46 04 21 11 | Laurent.Maveyraud(a)ipbs.fr <mailto:Laurent.maveyraud@ipbs.fr> | L. Maveyraud <https://fr.linkedin.com/in/laurent-maveyraud-8b394a5> | L. Maveyraud <https://orcid.org/0000-0003-4610-8319> UMR5089 | CNRS - UT3 | 205 Route de Narbonne BP 64182 - 31077 Toulouse Cedex 4 ipbs.fr <https://www.ipbs.fr/>| Team Website <https://www.ipbs.fr/structural-biophysics>| pict.ipbs.fr <https://cribligand.ipbs.fr/> @IpbsToulouse <https://twitter.com/IpbsToulouse> ipbs.cnrs <https://www.facebook.com/IPBS.CNRS/>

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ChimeraX-users April 2023