- ChimeraX-users - RBVI Mailing Lists

problem to open a swiss dock results file
by Aurélie Hoeffel 13 Aug '24

13 Aug '24

Dear Chimeras members, I would be interested to use chimera x for interpreting some results of my docking. I precise it is the first time I use swiss dock as well as chimera x, after receiving the swiss dock file in a tar.gz format, I compress it via 7Zip but then chimera x, is not able to process and open my document, ii is just written, tar data ,Unrecognized file suffix '.tar', so I do not kwo if the pb come from chimera or swiss dock, do you know how I can solve the problem? Thanks in advance, Aurelie

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ChimeraX-daily (1.9, 5 Aug 2024); Log panel stealing focus
by leeyang+chimerax＠gmail.com 10 Aug '24

10 Aug '24

Hi, Downloaded the above Daily (macOS 14.5, Universal), primarily for the workaround retrieving mmCIFs containing an underscore (#15557). I noticed that the Log toolpanel steals focus whenever it updates. Perhaps something that has already been dealt with? Otherwise, thought I should post it here. Cheers, Yang

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AlphaFold version in ChimeraX 1.8
by Anna Mestre Borras 09 Aug '24

09 Aug '24

Hi, I would like to confirm which is the AlphaFold version in ChimeraX 1.8 when using Tools --> structure prediction --> AlphaFold. Thanks! Best, Anna

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Could not display the lipid such as cardiolipin
by 杨雪梅 08 Aug '24

08 Aug '24

Dear ChimeraX support group, When I open my PDB with ChimeraX, some lipids (get from the coot library with three-code) could not be seen. When it open with pymol, the lipids were displayed normal. Have you met such problem and how did you fix it? Looking forward to your kind help. Sincerely yours, Xuemei Yang Chinese Academy of Sciences Shanghai Institute of Materia Medica

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Could not display the lipid such as cardiolipin
by Yang Xuemei 08 Aug '24

08 Aug '24

Dear ChimeraX support group, When I open my PDB with ChimeraX, some lipids (get from the coot library with three-code) could not be seen. When it open with pymol, the lipids were displayed normal. Have you met such problem and how did you fix it? Looking forward to your kind help. Sincerely yours, Xuemei Yang Fudan University Chinese Academy of Sciences Shanghai Institute of Materia Medica

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problem for the PDB deposition
by Yanhe Zhao 07 Aug '24

07 Aug '24

Dear ChimeraX community and developer, I am trying to deposit my map with model. I save the model from pdb to cif in ChimeraX because of large amount of atoms, then got error as "Missing '_entity_poly.pdbx_strand_id' item. I tired to use pymol to open my pdb and save it as cif by 'Export Molecule', in which I just use the default options. I checked the saved cif in ChimeraX, which is weird since it couldn't be show in cartoon style. Is there any easy to handle this in ChimeraX or any option should be used in the 'Export Molecule' in Pymol? Thanks and cheers, Yanhe

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Inverted fit in map ?
by GOVAERTS Cédric 07 Aug '24

07 Aug '24

Hi Team I would like to compare to conformations of a protein whose structures have been solved by cryoEM (conf1 with map1 and conf2 with map2) So I want to have the coordinates *and* the cryoEM maps aligned. Aligning the two conformations is easy thanks to matchmaker (align conf1 to conf2) However, I can I align map2 onto conf2 so that I can compare with map1 ? Basically I would like to do an “inverse” fit into map conf2->map2. Can I do that ? Note : I do not want to align map2 ontomap1 because of resolution and structural differences, the superimposition should be done at the coordinate level (actually on a subset of it which is easy in matchmaker). Thanks ! Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77<tel:+3226505377> Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

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Question regarding per-Residue RMSD
by Zimiao Meng 07 Aug '24

07 Aug '24

Dear Developers/Researchers of ChimeraX, I'm a student researcher trying to utilize ChimeraX to analyze structures of models predicted by programs. Currently, when I do matchmaker, only the RMSD value is displayed. I'd like to know the per-residue RMSD (which should also be the alignment error for that residue) for a section of the sequence that's a few hundred residues long. I wonder if there is a way to display the information that ChimeraX used to calculate the overall RMSD? Or would the only way to do it be writing a python script? Best, Zimiao

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Looking for scale
by David S. Fay 07 Aug '24

07 Aug '24

Hi, Does anyone know if a reference-type PAE bar exists for the ChimeraX PAE plot when using the Rainbow (orange/yellow/blue) selection? Something similar to what AF provides for the (green) scale (below) or the electro-charge (blue/white/red) maps? Rainbow provides a nice visual range, but I couldn't find an associated score reference. [cid:7001d3eb-43d0-4009-9596-6843ea44695a@namprd05.prod.outlook.com] Thanks, David

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ChimeraX website not accessible from time to time
by Roden Deng Luo 07 Aug '24

07 Aug '24

Hi, This has happened quite some times in the last few months. I realized just now that I could not access https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/core/logger.html. I then checked the following, and all were not working. Is this my own problem or a server-side issue? Is there an offline developer documentation (PDF or HTML)? https://www.cgl.ucsf.edu/chimerax/docs/user/commands/log.html https://www.cgl.ucsf.edu/chimerax/download.html https://www.cgl.ucsf.edu/chimerax/docs/licensing.html Many thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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