- ChimeraX-users - RBVI Mailing Lists

ChimeraX protein-protein binding site modeling question
by Parks, Ryssa 20 Dec '23

20 Dec '23

Hello, I work in a lab that researches biopesticides in the form of insect neuropeptides, which bind to receptor proteins. I am trying to use ChimeraX to model potential binding sites between peptide ligands and their corresponding receptor. Does ChimeraX have this capability? When I was trying to figure this out myself online through the ChimeraX Youtube tutorials and tutorials on the UCSF site, I came across a comment on a video that mentioned I could upload the sequences of my receptor and peptide ligand separated by a comma, and model it as a protein complex, and then I can get information on where the two molecules interact. I'm relatively new to protein research, and so I hadn't yet thought of ligand-protein interactions as a type of protein complex. My specific questions are: * When modeling a peptide ligand and a receptor as a protein complex, will ChimeraX accurately predict the relationship between the two molecules based on binding compatibility? Or is it based on something else, like similarity of sequence alignments...? * If multiple binding sites are possible, is there any way to view the different options for multiple binding sites? Or is there any way to restrict the area on the receptor to which my target peptide ligand is predicted to bind (i.e. the extracellular region only)? * The peptide ligands are only 7-9 amino acids in length and do not take very long to model, but the receptor is about 600 amino acids and takes a much longer time to model. Do I have to model protein complexes by re-modeling everything for each different receptor-ligand combination, or can I combine existing models somehow? I hope these questions aren't too troublesome, and I hope I haven't grossly misunderstood ChimeraX's capabilities. Thank you for your time, Ryssa Parks

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Problem with Snap Installation
by Stephen P. Molnar 20 Dec '23

20 Dec '23

I have had Chimerax.flatpack installed on by Debian Bookworm Platform. As a result of a system crash I was force to reinstall the OS. When I attempted a reinstallation on the New OS I got the following error: error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires the runtime org.freedesktop.Platform/x86_64/22.08 which was not found Please advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. https://insilicochemistry.net (614)312-7528 (c) Skype: smolnar1

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ISOLDE messes with view?
by Alexis Rohou 19 Dec '23

19 Dec '23

Hello, I've just noticed that the view command doesn't behave as expected after I have started ISOLDE. Specifically, if I save a view ("view name view1") and later try to restore it ("view view1"), it will get me back to the correct orientation of view1 but the zoom will not be restored. I assume ISOLDE is changing a setting under the hood. Is there some way to make ISOLDE play nicely with "view"? Right now my only workaround is to quit ChimeraX and start again front he beginning, without launching ISOLDE. Cheers, Alexis

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Adjust Torsions section of Build Structure is missing
by duhq 19 Dec '23

19 Dec '23

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Log auto-scrolling
by Alexis Rohou 19 Dec '23

19 Dec '23

Hi, Is there a way to make sure that the Log window stays scrolled all the way to the end of the log? I keep having to scroll back down to see the output of the last command I issued. Perhaps this is because I scrolled back up at some point, I'm not sure. Either way, it'd be nice to have the option to switch on (and off) "auto scroll" for the Log window. Cheers, Alexis

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Support for unknown amino acid and nucleotide
by Vorländer,Matthias Kopano 19 Dec '23

19 Dec '23

Dear ChimeraX team, When depositing models in the PDB, it is often necessary to change the nucleotide or amino acid type to “Unknown” when the resolution is not good enough to identify the register (https://www.wwpdb.org/documentation/procedure) Would it be possible to extend the functionality of the swapna and swapaa commands to support changing residues into UNK for proteins and N/DN for nucleic acids? Many thanks in advance, Matthias

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ChimeraX 1.7 release!
by Elaine Meng 19 Dec '23

19 Dec '23

UCSF ChimeraX version 1.7 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html Updates since version 1.6 (May 2023) include: New graphical interfaces: - Fetch By ID - Map Filter - Adjust Torsions (new section in Build Structure) - Adjust Angles defined by three atoms (also in Build Structure) Open command options to: - specify model number - combine incoming session with existing session - designate map as difference map (show +/-contours automatically) - fetch by IUPAC name (also in Build Structure tool) - fetch EMDB map + fit structures Mouse mode updates: - new mouse mode to center the view on the clicked item - better separation of trackpad multitouch zoom and rotate - Z-translation by additionally pressing Ctrl in a translation mouse mode Other: - invert selection with left/right arrow keys - mcopy command to copy settings from one atomic structure to another - save GLTF options to cull backfaces, omit per-vertex colors, omit normals - volume defaultvalues command to set defaults for subsequently opened maps - info command saveFile option (list selection, attribute values, etc.) - opening docking results automatically starts ViewDockX - button to save Blast Protein results to TSV For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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extract highlighted residue with sequence number
by paul.protein.test＠gmail.com 19 Dec '23

19 Dec '23

Hi All I am highlighting all residues that are involved in a protein-protein interaction. Is there anyway to extract a list including all residues and associated sequence number, or display in log?

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Re: extract highlighted residue with sequence number
by Luca Genz 19 Dec '23

19 Dec '23

Hi, there is a plug-in in the ChimeraX toolshed called PICKLUSTER that can identify the residues in the protein interface, colors them and reports a list of the residues in the interface with their sequence number in the Log. It can also report the contacts and can color the interface residues in the sequence. Hope that helps!

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how to set pH level from ChimeraX
by Chang Jang 18 Dec '23

18 Dec '23

Dear ChimeraX help, I am using ChimeraX 1.6.1. Would anyone know how to "*set or change and check*" a pH level of a protein or a system from the software? Thanks, Chang Woon

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