- ChimeraX-users - RBVI Mailing Lists

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 20 Dec '23

20 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 20 Dec '23

20 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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AUTODOCK VINA - CHIMERAX (Candidate version 1.7rc202312150000)
by Emmanuel Funsho Alakunle 18 Dec '23

18 Dec '23

Good day, Please I am running Chimera-x ( Candidate version 1.7rc202312150000) on windows11, and I cannot locate the autodock vina plugin. Kindly help. Thanks *Emmanuel Funsho Alakunle* *Natural and Environmental Sciences (Biomedical Science)* *American University of Nigeria* *Yola-by-pass, PMB 2250, Yola* *Nigeria.* *P:+234(0)8108074431* *Skype:* *Linkedin: **linkedin.com/in/emmanuel-alakunle-356088154 <https://www.linkedin.com/in/emmanuel-alakunle-356088154>*

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RAMACHDRAN PLOT - CHIMERAX
by Emmanuel Funsho Alakunle 17 Dec '23

17 Dec '23

Good day, Please I am running Chimera-x on windows11, and I cannot generate ramachdran plot. Kindly help. Thanks *Emmanuel Funsho Alakunle* *Natural and Environmental Sciences (Biomedical Science)* *American University of Nigeria* *Yola-by-pass, PMB 2250, Yola* *Nigeria.* *P:+234(0)8108074431* *Skype:* *Linkedin: **linkedin.com/in/emmanuel-alakunle-356088154 <https://www.linkedin.com/in/emmanuel-alakunle-356088154>*

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savefile command
by Bajaj, Ruchika 17 Dec '23

17 Dec '23

Hi I am trying to use the following commands for selected atoms. I am trying this "info atoms sel" and it is working. However, I am not able to use saveFile file commands. Could you please help me with its usage. I'd appreciate your help in this regard. Thanks !! Regards Ruchika info atoms atom-spec<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/atomspec.html> [ attribute attribute-name ] [ saveFile<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#saveFile> file ]

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Density map on ligand
by Louis Fellipe Moreno Oliveira 16 Dec '23

16 Dec '23

Hello, I hope this email finds you well. My name is Louis OIiveira, and I am a Master's student specializing in protein crystallography at the University of São Paulo. I am currently using Chimera X for generating images of the structure I am studying. However, I have encountered some issues that I am struggling to resolve. Specifically, I have successfully validated the structure of the enzyme and am now attempting to present the co-crystallized ligand along with its electronic density map interacting with the enzyme. My challenge lies in isolating the electronic density of the ligand without including the electronic density of the nearby residues. I have attempted to use the "zone" function in the map menu, but I am still seeing some electronic density that I wish to exclude as shown in the picture . I would greatly appreciate your guidance on how to effectively isolate the electronic density of the ligand in Chimera X. If you have any insights or recommendations, I would be grateful for your assistance. Thank you for your time, and I look forward to hearing from you soon. Best regards, Louis Oliveira Master's Student Instituto de Fisica de São Carlos University of São Paulo

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insertion codes in labels
by Alexis Rohou 14 Dec '23

14 Dec '23

Hello, A two part question from me today: Part A. What is the syntax to get the label command to show insertion codes? As far as I can tell, insertion codes are not attributes. I can see that the insertion code is part the residue ID, but I don't know how to specify it as part of the label command. Part 2. Would you consider having residue labels show insertion codes by default? This would be very useful when labeling residues from antibodies with Kabat numbering, for example, and my guess is it wouldn't "hurt" existing usage. My apologies to Elaine in advance if I missed all this in the documentation. Cheers, Alexis

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command line to save multiple models
by Rayees Mattoo 13 Dec '23

13 Dec '23

Hi, I volume flipped 20 different models (#1 to #20) and now I want to save all the 20 flipped maps as .mrc with the same name as before and add flip in their names. How could I modify the save command line to do that? Best

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'Send to Quest' button not available
by Wiesler, Marie-Christin (Manufacturing, Clayton) 12 Dec '23

12 Dec '23

Dear User Guides, I am trying to send a file from ChimeraX to LookSee, in order to visualise it on my Meta Quest Pro headset. The tool 'Send to Quest' is not available in ChimeraX on my desktop, it is supposed to be in Tools/General. Thanks in advance! Mary

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unexpected surface "shimmering" when model argument is given to turn command with soft lighting
by Alexis Rohou 12 Dec '23

12 Dec '23

Hi all, I was playing around with movies where I rotate models around their own centers and noticed an unpleasant (to my eye) rendering glitch. Steps to reproduce (this is with 1.7rc202311150127): close open pdb:7vja; lighting soft; surf; ~show; view movie record; turn y 1 360 model #1; wait 360; movie encode test_spin_model.mp4 movie record; turn y 1 360; wait 360; movie encode test_spin.mp4 So we have two "spin" movies of the same surface, but one of them ("test_spin_model.mp4") has a shimmering artefact. At first I mistook this for a video compression artefact, but it's there in the "live" rendering and it disappears if I drop the "model" argument to the "turn" command. Also, I can't reproduce this if I don't use soft lighting. I will try to send the movies as attachments to a reply to this email (not sure they'll go through). Cheers, Alexis

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rainbow "structures" different from single chain specifier
by vincent Chaptal 12 Dec '23

12 Dec '23

Hi, on a pdb ensemble, when I use: rainbow #1 structures palette blue:cyan it colors the whole chain 1.1 blue and varies the color to cyan all the way to chain 1.20 (which is what I want). However, if I want to color a specific chain differently using: rainbow #1.1-10/O palette red:yellow it colors the rainbow from N-ter to C-ter for all the chains. How can I apply the first type of coloring (structures) to a specific chain? Thank you. Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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augment mousemode center with cofr centerofview; alter animation frames
by leeyang+chimerax＠gmail.com 11 Dec '23

11 Dec '23

Hi, I find the mousemode center function very useful when navigating around a model. One of the features I loved about the original Chimera. Would it be possible to have the option to augment it with a cofr centerofview feature so that the pivotpoint then follows subsequent translation? Also, would it be possible to define a custom number of frames over which the animation occurs? Cheers, Yang

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Re: AlphaFold to run .pkl file and the tax error
by Tom Goddard 11 Dec '23

11 Dec '23

Hi Serhat, AlphaFold does not provide docking scores or energy minimization scores as far as I know. AlphaFold estimates pTM (predicted TM) and ipTM (interface predicted TM) scores related to prediction accuracy. You might want to google molecule TM score to learn about those. And googling Alphafold iptm gives as the top hit a paper describing those scores Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes https://academic.oup.com/bioinformatics/article/39/7/btad424/7219714 ChimeraX does not show you those scores but does have ways of visualizing the pLDDT (predicted local distance difference test) and PAE (predicted aligned error) generated by AlphaFold, described here https://www.rbvi.ucsf.edu/chimerax/data/pae-apr2022/pae.html And you may be interested in ChimeraX videos about visualizing AlphaFold confidence https://youtu.be/oxblwn0_PMM https://youtu.be/TMcjEecFHaI and more ChimeraX AlphaFold videos here https://www.rbvi.ucsf.edu/chimerax/docs/videos/ The .pkl (Python pickle) files contain data such as PAE scores. ChimeraX can read pkl file to show the scores as described in the above links. The alphafold issue #629 you reference about AlphaFold inserting jax data structures into .pkl files was long ago fixed in both AlphaFold and ChimeraX 1.5 as described in the link you sent. The solution is of course to update the version of ChimeraX and AlphaFold you are using. If you are using any ChimeraX version to run AlphaFold it is using a current AlphaFold. But ChimeraX AlphaFold runs don't produce .pkl files so I guess you are running an old AlphaFold in a different. Tom > On Dec 11, 2023, at 4:23 AM, serhat inceer <serhatinceer(a)yahoo.com> wrote: > > Dear Tom Goddard > > > My name is Serhat Inceer Researcher at the University of Vienna department od Molecular Biology, and I am reaching out to seek assistance regarding the interpretation of docking scores and multimer energy minimization scores in AlphaFold. > > Additionally, I have questions about running ".pkl" files to analyze plDDt graphs for the predicted and ranked models that I have already predicted models. > > Specifically, I am interested in understanding the methodology and significance of the docking score and multimer energy minimization score provided by AlphaFold. Could you please provide more information on how these scores are calculated and what they signify in the context of protein structure prediction? > > Furthermore, I have generated ".pkl" files for my predicted models, and I am interested in running them to obtain plDDt graphs. Could you please guide me on the steps to run the ".pkl" files for this purpose? Any documentation or resources that outline the process would be greatly appreciated. > > According my research on GitHub you got also same error and I am wondering about how could you fit it this situation > > https://github.com/google-deepmind/alphafold/issues/629 > > Thank you very much for your time and assistance. I look forward to your response. > > Best regards, > > Serhat Inceer > >

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Smooth-MD script for a trajectory visualisation
by Enrico Martinez 08 Dec '23

08 Dec '23

Dear Chimera-X users. I am trying to record a md trajectory loaded as multi-pdb file: open ./stripped_traj2.pdb coordsets true I have the issue with smooth-md script (enclosed), which produces the following error: open smooth_md_chX.py open /home/test/Bureau/MOVIE_CHIMERAX\/smooth_md_chX.pyTraceback (most recent call last): File "/home/test/Bureau/MOVIE_CHIMERAX\/smooth_md_chX.py", line 23, in <module> avg += weight * coord_sets[j] ValueError: operands could not be broadcast together with shapes (6120,3) (6112,3) (6120,3) Should something be fixed in the script in order that I could observe the MD movie with smooth details ? Thank you in advance Enrico

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Re: Following Up on Drawing Outlines
by Tom Goddard 07 Dec '23

07 Dec '23

Hi André, There is only one selection outline in ChimeraX so you cannot show different color outlines directly in ChimeraX using the selection outline. Here are a couple ideas. You could select all your sites and make one outline around all of them in green and then in Photoshop change the color of parts of the outline to the appropriate colors. Another idea is you can select each patch and make its outline in the correct color and then just save that outline but not the surface. To show just the outline and not the surface you would make the surface 100% transparent and hide atoms transparency 100 hide atoms save outline1.png transparentBackground true. Save each outline as a separate image and then layer them on top of your surface in Photoshop. A problem with both of these methods is that your patches border each other so the outlines will overlap. In fact the selection outline extends outward when you make it thicker (ChimeraX avoids covering the patch with the outline). So two adjacent patches with different outlines are going to draw the outlines intersecting and crossing each other where they adjoin each other. Making the outlines extend inward could be done in Photoshop by fattening the individual layer outlines. This gets into a lot of hand work. Tom > On Dec 7, 2023, at 1:15 PM, Andre Leon <aleon(a)scripps.edu> wrote: > > Hello Tom, > > Thank you for the response! I'm guessing the answer to my next question is no, but I was wondering if there's a way to create these selection outlines around multiple regions to create figures similar to the one below, highlighting all the major antigenic sites on influenza HA. That way I can simultaneously outline the epitopes and also color the figure by sequence conservation as opposed to doing one or the other. If that's not possible, than I will pseudo outline in Illustrator or Photoshop, but it would be ideal to be able to specifically highlight the exact residues using ChimeraX. > > Again, thank you so much for your rapid response! > > > Best Regards, > André Nicolás León > Graduate Student - Ward Lab <https://ward.scripps.edu/> > https://www.linkedin.com/in/andrenicolasleon/ > From: Tom Goddard <goddard(a)sonic.net> > Sent: Thursday, December 7, 2023 12:25 PM > To: Andre Leon <aleon(a)scripps.edu> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] Following Up on Drawing Outlines > > Hi André, > > Making a thick colored outline around an epitope on a protein surface is easier in ChimeraX using thick selection outlines. The link you mentioned from 2014 is from our old program Chimera which could only draw thin 1 pixel wide outlines. Here is an example in ChimeraX where I make a thick (10 pixel wide) red outline around some residues. > > open 2x7r > hide ~/C atoms > surface /C > select /C:670-681 > graphics selection color red width 10 > > Tom > > > >> On Dec 7, 2023, at 10:53 AM, Andre Leon via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hello Chimerax, >> >> I was wondering if there has been any progress on making outlines of specific epitopes in ChimeraX since this thread back in 2014? <https://www.cgl.ucsf.edu/chimera/data/outline-may2014/outlines.html> Thank you in advance. >> >> Best Regards, >> André Nicolás León >> Graduate Student - Ward Lab <https://ward.scripps.edu/> >> https://www.linkedin.com/in/andrenicolasleon/ >> _______________________________________________ >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

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Following Up on Drawing Outlines
by Andre Leon 07 Dec '23

07 Dec '23

Hello Chimerax, I was wondering if there has been any progress on making outlines of specific epitopes in ChimeraX since this thread back in 2014?<https://www.cgl.ucsf.edu/chimera/data/outline-may2014/outlines.html> Thank you in advance. Best Regards, André Nicolás León Graduate Student - Ward Lab<https://ward.scripps.edu/> https://www.linkedin.com/in/andrenicolasleon/

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Add charge to PDB fails
by Daniel Hsu 06 Dec '23

06 Dec '23

Hi All What might cause this action to fail, pH=7.4, H added to protein before adding charge? No errors were thrown. Both DOCK-Prep, and adding H then charge both do not change the PDB file (no charges added to respective atoms). Log reports "Using Amber 20 recommended default charges and atom types for standard residues" Alternative command 'addcharge standardizeResidues 5BU,CSL,MSE,UMS' reports "Using Amber 20 recommended default charges and atom types for standard residues" and no errors but don't add charges to saved PDB file. Charges are added with another structure editor. Thanks for insights! **CONFIDENTIALITY NOTICE** This e-mail communication and any attachments are for the sole use of the intended recipient and may contain information that is confidential and privileged under state and federal privacy laws. If you received this e-mail in error, be aware that any unauthorized use, disclosure, copying, or distribution is strictly prohibited. If you received this e-mail in error, please contact the sender immediately and destroy/delete all copies of this message.

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Surphace representation of multi-model pdb and moovie recording
by Enrico Martinez 06 Dec '23

06 Dec '23

Dear Chimera-X users ! I am working on molecular visualization of membrane system from the md trajectory loaded in the Chimera-x using the open coordset true command. The issue is with the surface representation of the membrane: transparency :OL,PA,PE,PC 80 target s which are applied only on the current frame (not on the whole trajectory). Also when I try to make a movie of the system the presence of the surface does slow down everything. Which options could be useful e.g. to decrease the quality of the surface representation ? Many thanks in advance Enrico

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