July 2024 - ChimeraX-users - RBVI Mailing Lists

initial dark mode support
by Greg Couch 16 Dec '24

16 Dec '24

FYI, the ChimeraX daily build now has dark mode support. So if you set your desktop to use dark mode, ChimeraX should follow. It's a work in progress, and it depends on developer's making their code dark mode aware (eg., icons may need to be modified), but if you notice any black text on a dark background, please let me know. -- Greg

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ChimeraX 1.8 release
by Elaine Meng 10 Dec '24

10 Dec '24

UCSF ChimeraX version 1.8 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 1.7 (Dec 2023) include: - show worm depictions of attribute values (B-factor, conservation, etc.) using Render by Attribute tool or "cartoon byattribute" command - show attribute values with atomic radii using Render by Attribute or "size byattribute" - Select by Attribute graphical interface - Join Models generalized to any covalent bond (not just peptide) - show multiple alternate locations simultaneously with "altlocs show" - "pbond" command to create arbitrary pseudobonds - "measure contactarea" to report the area of one surface within a cutoff distance of another - Segmentations tool for interactive manual segmentation in 2D slice views, 3D (desktop), or 3D (VR) can be applied to any volume data, not just medical images; several fixes and ergonomic improvements including icons to assign/deassign mouse and VR hand-controller modes with a single click - set up and analyze batch AlphaFold predictions to search for protein-protein interactions (commands for advanced users who can run ColabFold directly on Linux) support for: - reading predicted aligned error (PAE) data from AlphaFold 3 - reading docking results from MOE - fetching atomic structures and maps from PDB-REDO - fetching/display of PDB NMR-STAR restraints 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 Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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color bfactor by alphafold palette
by Agnieszka Obarska 11 Nov '24

11 Nov '24

Hi, I’ve just would like to let you know that we’ve noticed recently that alphafold palette in ChimeraX is not consistent with original AlphaFold coloring. Please see the slide attached. On the left there is a model colored by the “color bfactor pal alpha” command in ChimeraX while on the right there is the same model colored according to AlphaFold coloring scheme. Best, Agnieszka

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Ribbon style editor
by Alessio Nocentini 09 Sep '24

09 Sep '24

Hello, I have been an academic user of chimera for years. I have just downloaded chimerax but I cannot find the ribbon style editor. Can you please help? Best regards Alessio -- Dr. Alessio Nocentini University of Florence Neurofarba Department Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685 *NEUROFARBA Dipartimento di **ECCELLENZA 2023-2027*

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August 1 Chimera(X) website downtime
by Elaine Meng 01 Aug '24

01 Aug '24

Planned downtime for server maintenance: The Chimera and ChimeraX websites, Toolshed, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable August 1, 3-6 pm PDT. Apologies for any inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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seeking AlphaFold advice
by Elaine Meng 30 Jul '24

30 Jul '24

Hi David, Please send questions to the chimerax-users address CC'd here instead of to me individually. I am not an AlphaFold expert, whereas maybe others on the list can answer your questions. I removed your link because I didn't know if you were willing to share it publicly. If so, please repost to the group (chimerax-users address CC'd here). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 30, 2024, at 6:26 AM, David S. Fay <DavidFay(a)uwyo.edu> wrote: > > Thanks for that information Elaine. That is my take as well, but I know much less about these things… > > On a slightly different note, I really wish there was an alphafold “best practices” tutorial or methods paper. Mainly I’m focused on protein-protein interactions, which is something I think many people are interested in. I gave a talk to my department recently, where I tried to do some of this. But because this isn’t my area, I rather feel like this is a case of the slightly blind leading the even-more blind. Still, I’ve attached a link to a google folder that contains my talk. I’d love to get feedback on this from experts in the field, such as folks at ChimeraX. > > And one last question, which you might have an opinion about. Is AF3 any good at predicted changes in structure with amino acid substitutions? I know that AF2 was not, but given that AF3 includes secondary modifications, it would seem like this capability should be improved? Especially if it’s relying less on MSAs. For that matter, do the folks at ChimeraX have an opinion about how AF3 alters structure and interactions based on modifications like phosphorylation? > > Thanks, > > David

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Hide axis indicator
by Hantz, Eric 30 Jul '24

30 Jul '24

Hello, I am using ChimeraX 1.8 macOS, and I am having trouble finding a way to hide the axes indicator. I am trying to make a figure of a ligand bound protein structure with the electron density shown for the ligand. The best I can have been able to do is make the axes indicator slightly transparent but it is still visible. Thanks, Eric

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Re: Answer to question regarding Consurf and ChimeraX
by Elaine Meng 29 Jul '24

29 Jul '24

Hi David, There is no option to call the ConSurf web service from inside ChimeraX (or Chimera), I just meant to ask whether you could display the output in ChimeraX. I didn't know the recent version of the ConSurf server provided ChimeraX sessions, so that is helpful, thanks! You would have to talk to the ConSurf website developers about what information they put into the session. However, I would not expect it to have any Alphafold information (pLDDT or PAE values). It probably just has whatever atomic coordinates you uploaded (if that's how you input the structure), or atomic coordinates straight from the PDB. Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 26, 2024, at 8:04 PM, David S. Fay <DavidFay(a)uwyo.edu> wrote: > > Hi Elaine, > > I was able to open the ConSurf .cxs files using ChimeraX, which were part of the Consurf download. I have tried using ConSurf through Chimera or ChimeraX yet. I’ve attached an example image I recently obtained using ChimeraX. One limitation I haven’t worked is how to display PAE contacts between peptides when using this ConSurf file in ChimeraX. I can do it with AF2/3 files – no problem, but not with the ConSurf files. Also, the .cxs files don't seem to work for other ChimeraX functions, such as: hide @@bfactor<50 ribbon. It’s also unfortunate that ConSurf doesn’t allow you to visualize conservation for more than one of the two peptide chains, at least as far as I can tell. But it’s still quite useful. > > If you have any additional hints I’d be glad to try them. > > David > > > > <Screenshot 2024-07-26 at 8.54.04 PM.png> >> On Jul 26, 2024, at 3:11 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi David, >> Thanks for the info about the ConSurf website. Did you ever use the ConSurf website output in ChimeraX or were all the outputs only suitable for Chimera (which was my experience)? >> >> Some other notes, in case you or others didn't know... >> >> (1) ChimeraX also plots PAE data from AlphaFold2 or AlphaFold3 >> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#pae> >> >> example command: >> alphafold fetch LDLR_HUMAN pae true >> >> screenshot of result: >> <Screen Shot 2024-07-26 at 2.10.24 PM.png> >> >> (2) ChimeraX can convert mmCIF to PDB, i.e. you could just open the mmCIF file and then save the structure as PDB. Can be done with the File menu or with the commands "open" and "save": >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html> >> >> Elaine >> >>> On Jul 26, 2024, at 1:54 PM, David S. Fay via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> Real quick followup for those who might be interested. >>> >>> I did contact ConSurf. They suggested using a different browser and clearing the cache. I did both and it now works but only on Chrome and NOT on Safari (for those using Macs). This isn’t the first time I’ve had problems with Safari. ConSurf is helpful for looking at conservation of a protein sequence and/or a 3D structure. >>> >>> Incidentally, for converting cif to pdb, which is necessary for ConSurf, this site worked well. >>> https://project-gemmi.github.io/wasm/convert/cif2pdb.html >>> >>> Also, some may be interested in using this site to generate AF2-like red/blue PAE diagrams as well as creating spreadsheets of predicted peptide interactions from AF3. >>> https://predictomes.org/tools/af3/ >>> >>> David >>> >>>> On Jul 25, 2024, at 9:42 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>> >>>> ◆ This message was sent from a non-UWYO address. Please exercise caution when clicking links or opening attachments from external sources. >>>> >>>> >>>> Hi David, >>>> Did you try asking the Consurf developers? There is a "contact us" link on their website: >>>> >>>> <https://consurf.tau.ac.il/consurf_contact.php> >>>> >>>> I haven't used this web service recently. I have only used its outputs in Chimera so far (never ChimeraX). >>>> >>>> If I go to a page for precalculated results there is a "Chimera" download that gives a Chimera session (.py file), e.g. >>>> >>>> <https://consurfdb.tau.ac.il/main_output.php?pdb_ID=2GBP&view_chain=A&unique…> >>>> >>>> I tried downloading that just now, and it works in Chimera. In Chimera you can use File... Export Scene... and export a .py file that you can open with ChimeraX. Only the ribbon and carbon atoms are colored by the Consurf values, however, not the heteroatoms. >>>> >>>> I hope this helps, >>>> Elaine >>>> ----- >>>> Elaine C. Meng, Ph.D. >>>> UCSF Chimera(X) team >>>> Resource for Biocomputing, Visualization, and Informatics >>>> Department of Pharmaceutical Chemistry >>>> University of California, San Francisco >>>> >>>> >>>>> On Jul 24, 2024, at 8:08 PM, David S. Fay via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>>> >>>>> Hi, >>>>> >>>>> I’m curious if anyone else is having trouble getting results from ConSurf? The site appears to be up, which maybe wasn’t the case a while back. But trying various kinds of inputs doesn’t lead to any results. Rather, it just seems to just get hung up. (It’s also possible I’m doing something incorrectly.) >>>>> >>>>> Thanks in advance! >>>>> >>>>> David >>>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> >

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Doubt about volume cropping
by Leyre Marin Arraiza 29 Jul '24

29 Jul '24

Dear UCSF ChimeraX, I have a practical question regarding 3D volume visualization and cropping in ChimeraX. I have a big 3D density map which includes the densities for several models of different proteins. To facilitate visualization and model building, I would like to crop the density map, so that it includes only two of the models. Is it possible to crop my density map around those models, to make it a bit smaller and more focused on the areas of interest? Hope I am explaining myself. Thanks and best regards, Leyre Leyre Marin Arraiza PhD fellow University of Copenhagen Novo Nordisk Foundation Center for Protein Research Taylor Group Blegdamsvej 3B, Building 6, 6-1-10 2200 København N leyre.arraiza(a)cpr.ku.dk<mailto:leyre.arraiza@cpr.ku.dk> [CvwfJbQuv4S75bEAAAAASUVORK5CYII=] How we protect personal data<https://informationssikkerhed.ku.dk/english/protection-of-information-priva…>

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ChimeraX adjacent question about ConSurf
by David S. Fay 26 Jul '24

26 Jul '24

Hi, I’m curious if anyone else is having trouble getting results from ConSurf? The site appears to be up, which maybe wasn’t the case a while back. But trying various kinds of inputs doesn’t lead to any results. Rather, it just seems to just get hung up. (It’s also possible I’m doing something incorrectly.) Thanks in advance! David David S. Fay Ph.D. Professor, Department of Molecular Biology Associate Director, National Institutes of Health Wyoming INBRE University of Wyoming davidfay(a)uwyo.edu

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