- ChimeraX-users - RBVI Mailing Lists

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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ChimeraX & ConSurf
by martin.brehm＠univie.ac.at 05 Dec '23

05 Dec '23

Dear ChimeraX developers, I have a question regarding a potential upgrade of ChimeraX. Would it be possible to include the functionality of ConSurf, a tool to plot the degree of sequence conservation onto a model, into ChimeraX? The code for this is publically available on GitHub: https://github.com/Rostlab/ConSurf See this publication for more information: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987940/ Thanks a lot in advance and have a nice day! Best regards Martin Brehm Martin Brehm - PhD Student Falk Lab - Max Perutz Labs Vienna Room 1.624 - Phone +43 14277 74361 martin.brehm(a)univie.ac.at

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ISOLDE on Mac M1/M2/M3 or on Linux CentOS 7
by Mark Hilge 05 Dec '23

05 Dec '23

Hello, Could you please tell me whether your latest Version of ISOLDE would either run on a Mac with an Apple Silicon chip (M1, M2, or M3) or on a Linux box with CentOS 7 installed? Many thanks in advance! Kind regards, Mark

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Missing tools in ChimeraX
by Lars Backman 05 Dec '23

05 Dec '23

Hi, In Chimera, a tool named “Viewing” was available. It was an excellent tool to adjust appearance of the final png or jpg figure. I have looked for a similar tool in ChimeraX, but it seems to be absent. Or is there a way to create something similar? Best regards, Lars Backman [signature_2226121467] Lars Backman Professor Department of Chemistry, Biochemistry Umeå University SE-90187 Umeå, Sweden Tel: (46) 070 833 9946 e-mail: lars.backman(a)chem.umu.se<applewebdata://6E905793-FDA7-4651-8DC6-A97D8021B9DD/lars.backman@chem.umu.se> http://staff.chem.umu.se/lars.backman/research/ När du skickar e-post till Umeå universitet så innebär detta att Umeå universitet behandlar dina personuppgifter. För att läsa mer om hur detta går till, gå till www.umu.se/gdpr<http://www.umu.se/gdpr> By sending an email to Umeå University, the University will need to process your personal data. For more information, please read www.umu.se/en/gdpr<http://www.umu.se/en/gdpr>

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Exporting scene with .obj and .mtl file
by Berndsen, Zachary 04 Dec '23

04 Dec '23

Hello, I need to export an obj file along with the associated mtl file, however, under the “file > save” option, there is only an option for saving as .obj, not .mtl. I read in the online documentation that there should be the capability to “export a scene” which saves an obj and mtl file, however I do not see this option when using v 1.6.1. Is this still supported? Thanks, Zack

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Python Function that implements the "center" method from the GUI
by tong.you＠icm.uu.se 01 Dec '23

01 Dec '23

Hello, For an automatic pipeline workflow, I want to have a way to center several mrc files using the Python module. However, I can't seem to find the corresponding Python function that I can use in a script to "center" an opened map. Is there a Python function to "center" a map similarily as in the GUI? Kind regards, Tong

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Independent movement of chains in movie
by Caroline Stone (JIC) 30 Nov '23

30 Nov '23

Dear ChimeraX team and list subscribers, I am making a little movie to show a complex of two proteins, but am stuck on individual movements of chain /A and /B. If I use the move command, chain /A and /B both move independently, away from each other: move x -10 atoms /A; move x 10 atoms /B However, if I attempt to do the same movement by going -1 or +1 over a series of 10 frames, I no longer get any movement of /A and /B. move x -1 10 atoms /A; move x 1 10 atoms /B I can achieve movement over a number of frames, but both chains move although I tried to specify only /A. I did this based on "move axis [ distance [ frames ]]". move x -1 10 atoms /A I feel I might be on the right track because when I use turn, I am able to trigger simultaneous independent rotation of /A and /B around their own axes (thank you for this feature by the way, last time I wondered about this it wasn't possible). cofr /A; turn y -1 90 atoms /A; cofr /B; turn y 1 90 atoms /B My ultimate goal is to open the binding interface up a bit like opening a book. I suppose I could achieve a similar effect by setting the centre of rotation for each chain behind, rather than within - if independent movement over a series of frames isn't possible, I might experiment with that. I updated to version 1.6 and searched the list, but I still see this behaviour with the move command. Perhaps I am missing something basic? Thank you for any pointers you might be able to share! Caroline

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"view" in command line vs. menu
by C. Klein 30 Nov '23

30 Nov '23

Dear Eric, Oliver, et al. you may remember my comment on the missing "focus" function. Anyhow, what I noticed now is interesting: The function of the "view" command is different in the menus vs. the command line. in the command line, "view" will zoom out and show everything in the menu, "view" will focus on the selected ligand or whatever (which is what I want a bit more, mostly) Perhaps this could be resolved with modified or rather re-surrected terminology: Focus on selection: "focus" in command line "focus on selection" in menu Zoom to fit all: "zoomall" in command line "zoom to fit all" in menu just some suggestions. But what I think is clear is that the function of commandos should be identical in menu and command line. Again, thank you very much for your important and good work on the Chimera software. Best wishes Christian OpenGL version: 3.3.0 NVIDIA 452.56 OpenGL renderer: Quadro P620/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_US.cp1252 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: windows Manufacturer: LENOVO Model: 30C5004VGE OS: Microsoft Windows 11 Pro (Build 22621) Memory: 17,010,716,672 MaxProcessMemory: 137,438,953,344 CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2023.5.7 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 comtypes: 1.1.14 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pywin32: 305 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 WMI: 1.5.1 zipp: 3.15.0 -- Prof. Dr. C. Klein; c.klein(at)uni-heidelberg.de Medicinal Chemistry Institute of Pharmacy and Molecular Biotechnology IPMB Heidelberg University, INF 364 D-69120 Heidelberg Germany Phone: ++49-6221-54-4875 FAX : ++49-6221-54-6430

3 2

How to save a sequence in an mmCIF file?
by Guillaume Gaullier 29 Nov '23

29 Nov '23

Hello, Starting from an AlphaFold prediction, I refined a model against a map with ISOLDE. I trimmed the segments not supported by any density. The resulting mmCIF file that I saved now opens with this warning: Unknown polymer entity '1' near line 187 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Displaying the sequence of this chain shows the correct numbering (with jumps in numbering according to missing segments in the structure), but the sequence of the missing structure segments is not displayed. When I open the fasta file containing the full-length sequence, the sequence gets automatically associated to the structure, and the sequence viewer annotates the segments with missing structure correctly. I would like to save this full-length sequence in my mmCIF file so the full-length sequence with annotated missing structure segments shows up next time I open this file. But when I try to save at this point, I get the following notice: Not saving entity_poly_seq for non-authoritative sequences The documentation for "save" and "sequence" didn't help. How can I make this sequence "authoritative" and save it into my mmCIF file? 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

1 0

transition dipole moments
by gennaro.pescitelli＠unipi.it 28 Nov '23

28 Nov '23

Dear developers, first of all, thnak you for your great software, I just started using it. My question: is there a way to plot transition moments (electric and magnetic), as calculated e.g. by TD-DFT calculations in ORCA or Gaussian? If not directly from a log/out file, is tehre a way to manually add a vector arrow? Thanks Rino Pescitelli

3 7

Inquiry Regarding Feasibility of Implementing Protein Operations in Python
by g0423019 g0423019 28 Nov '23

28 Nov '23

Sorry. The earlier email by ms04000106(a)gmail.com was not sent using a university email address. It has been resent using the university email address. Dear UCSF ChimeraX, I hope this email finds you well. My name is Mayu Shibuya, and I am a student at Iwate University, currently affiliated with the wet biology laboratory. I am reaching out to seek guidance on the feasibility of utilizing the software for a specific task. Specifically, I am interested in performing addh and addcharge operations and automating these processes using a Python script. However, I do not know whether the addh and addcharge operations can be executed in Python. Could you kindly provide guidance on the possibility of achieving this with the software? If it is indeed feasible, I would greatly appreciate any instructions or methods you recommend for implementing these operations in a Python script. Thank you for taking the time to consider my inquiry. I greatly appreciate your assistance and look forward to hearing from you soon. Best regards, Mayu Shibuya Iwate University g0423019(a)iwate-u.ac.jp

3 2

Inquiry Regarding Feasibility of Implementing Protein Operations in Python
by 澁谷まゆ 28 Nov '23

28 Nov '23

Dear UCSF ChimeraX, I hope this email finds you well. My name is Mayu Shibuya, and I am a student at Iwate University, currently affiliated with the wet biology laboratory. I am reaching out to seek guidance on the feasibility of utilizing the software for a specific task. Specifically, I am interested in performing addh and addcharge operations and automating these processes using a Python script. However, I do not know whether the addh and addcharge operations can be executed in Python. Could you kindly provide guidance on the possibility of achieving this with the software? If it is indeed feasible, I would greatly appreciate any instructions or methods you recommend for implementing these operations in a Python script. Thank you for taking the time to consider my inquiry. I greatly appreciate your assistance and look forward to hearing from you soon. Best regards, Mayu Shibuya Iwate University ms04000106(a)gmail.com

1 0

hide dust
by Andrea Smith 28 Nov '23

28 Nov '23

Hi, I have cartoon and map visible for a part of my molecule (one protomer from a tetramer). When I click on hide dust, the dust is hidden but at the same time the map appears for the rest of the tetramer. Is there a way to hide dust around the visible part of the map while keeping a part of the map hidden? Thanks, Andrea

3 4

(no subject)
by Murphy, Kenneth 26 Nov '23

26 Nov '23

Hi, Would there be a way to save convservation scores from a large multiple sequence alignment into a file that could be re-loaded later instead of having to reload the actual alignment file? In looking at WDFY4, the alignment of the 3124 residue protein from 523 different species, the alignment fasta file takes around 10 minutes to load. After calculating the scores, the program shows the alignment and then the showing the convervations of residues in the protein is my goal of analysis. But it takes the same 10 minutes every time I open the session. I haven't found a way to save the scores themselves and load that in directly. Is there a way to do that? thanks it's a great program. ken murphy ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

3 3

Reading .xyz vs. Orca .out file
by Michael Patzschke 23 Nov '23

23 Nov '23

Dear colleagues, Recently the following problem has appeared: When I open an orca output file and chose the ball and stick option for displaying molecules, the radii of the balls are all wrong. This problem does not show up when I open the corresponding .xyz file. I try to attach an example to illustrate the problem. I would appreciate any help in this matter. Kind regards, Michael Patzschke __________________ Dr. Michael Patzschke Institute of Resource Ecology Chemistry of the f-elements Theoretical Chemistry Helmholtz-Zentrum Dresden - Rossendorf e. V. Telefon: +49 (0351) 260 2989 E-Mail: m.patzschke(a)hzdr.de <mailto:p.kaden@hzdr.de> Web: http://www.hzdr.de <http://www.hzdr.de/> Addresse: Bautzner Landstrasse 400 | 01328 Dresden Vorstand: Prof.Dr. Dr. Sebastian M. Schmidt, Dr. Diana Stiller Vereinsregister: VR 1693 beim Amtsgericht Dresden

3 3

Dialog box after dockprep command in 1.7rc202311210000
by r.m.newlon＠gmail.com 22 Nov '23

22 Nov '23

Hello all, I am on an Apple M1 and have just updated to ChimeraX 1.7rc202311210000. I am just starting to learn how to use ChimeraX from the command line (Terminal). My code that ran from Terminal on ChimeraX 1.6 doesn't seem to be working now with 1.7. Specifically, it seems that the dockprep command now ends by automatically popping up a dialog box prompting you to save a Mol2 file. I think this is causing problems when I try to run in nogui mode. I will include the "error message" at the end of this message, in case it is helpful. If this dialog box is the problem, is there a way to suppress it? Thank you! RN ==== Copied from Terminal ==== ... Dock prep finished Unexpected exception, save your work and exit: Traceback (most recent call last): File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/nogui.py", line 232, in execute self._cmd.run(text) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 168, in dock_prep_cmd dock_prep_caller(session, structures, memorization=memorize, nogui=True, **kw) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 144, in dock_prep_caller run_steps(session, state, structures) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 159, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/prep.py", line 107, in prep callback(session, state, structures) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 159, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/dock_prep.py", line 56, in run_for_dock_prep callback(session, state, structures) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 159, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/dock_prep.py", line 58, in run_for_dock_prep callback(session, state, structures) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 154, in run_steps callback() File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/prep.py", line 101, in postscript show_save_file_dialog(session, format=session.data_formats.save_format_from_suffix(".mol2").name) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog _dlg.display(session, **kw) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 31, in display parent = session.ui.main_window ^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'UI' object has no attribute 'main_window'

2 1

ChimeraX-users email frequency
by Siyoung Kim 22 Nov '23

22 Nov '23

Hello, Is there a way to control the frequency of receiving emails from chimerax-users (e.g., once a day, once a week, or once a month)? Thank you. Best, Siyoung

2 1

(no subject)
by Murphy, Kenneth 21 Nov '23

21 Nov '23

Thanks for ChimeraX. I've been loading multiple sequence alignments in fasta format directly into ChimeraX for mapping conservation onto a pdb and it works great. My MSA are directly from clustalo omega and in fasta format not clu formtat. My question is this. My compiled al2co.c as well as the binary I downloaded for al21co.exe doesn't work with input in fasta format. And yet ChimeraX opens and al2co window when I input my alignment. Does ChimeraX use another version of al2co that is configured to open fasta files? thanks for any info. ken murphy ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

2 2

Sequence via remotecontrol?
by Boris Steipe 21 Nov '23

21 Nov '23

Hi all - I am using the fantastic remotecontrol REST interface in teaching, and I have hit a surprising snag: is it not possible to return the sequence of a selection through the interface? What I need to do is align fragments of sequence I have obtained from external annotations (RADAR in this case), with the SEQRES derived sequence to match the sequence numbers to each other - generally they are not the same. I think I could write FASTA to a file with "save" and process that, and I think I could capture the output of "info" and parse that through a function, but I am wondering if there is not a way to get the sequence directly as a return value? Thanks! Kind regards, Boris

2 1

VR on/off button
by Steffen Thomas 21 Nov '23

21 Nov '23

Hello I'm currently looking into the interesting possibilities of ChimeraX and VR. As I am in a different room to my PC with my glasses, I access the PC desktop via SteamVR with ChimeraX open and start vr on in the command line. This works quite well with a virtual keyboard from SteamVR. Now I'm missing two things so far, which I probably just haven't found yet (I'm a VR newbie even though I've owned a GearView for some time now, but its capabilities are quite limited). Firstly, a virtual keyboard where I can enter commands in the command line with the blue or yellow cylinders (I have now found the command line in vr) and a button in the toolbar (for example in the Molecule Display area) that switches vr on or off, in the same way for example as show and hide ribbon. Are there any possibilities to realize this via python itself? Or plans to integrate something like this? Many thanks to the great ChimeraX community and all those responsible. Steffen --------------------------------------------------------------------------------------------------------------- Steffen Thomas

2 1

measure rotation showAxis does not create a measurable object
by Alexis Rohou 20 Nov '23

20 Nov '23

Hello again, I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes. Two of my axes are #4 and #5. When I try to measure the angle with "angle #4 #5", I get the error: "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)" I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related. Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable? Cheers, Alexis

4 12

Startup cxc scripts
by Siyoung Kim 20 Nov '23

20 Nov '23

Hello, Would there be a way to run some chimerax scripts at the beginning of every ChimeraX session? In particular, I want three things: 1. Change the color of the background. set bgColor white 2. Change the mode of the mouse. ui mousemode right zoom 3. Open the shell. ui tool show Shell The most relevant documentation I found was: "Python files in the directory *~/chimerax_start* (where *~* is the user's home directory) are imported automatically at startup." I put ChimeraX scripts (not python files) in this folder, but no luck. Thank you. Best, Siyoung

2 2

Tutorial
by Mark Rosenberg 20 Nov '23

20 Nov '23

Do you have a tutorial for ChimeraX generating publication quality surface and mesh maps with a docked model, please? Thanks Dr Mark F Rosenberg

3 4

specify id of output of define command
by Alexis Rohou 17 Nov '23

17 Nov '23

Hello, I've been scripting quite a bit with the define command of late, and I wonder if you might consider adding "id" or "modelId" to the set of general options available for this command, so that we could specify the ID of the object that is created. The current workaround is to use rename, which works but is a bit cumbersome. Given that many other commands allow us to specify ID of output objects, I figure it'd be nice for that pattern to apply here. Cheers, Alexis

2 2

Feature request: replace residues in model with residues from other model
by Vorländer,Matthias Kopano 16 Nov '23

16 Nov '23

Dear ChimeraX team, Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted. Many thanks in advance, Matthias

7 17

plane-spec
by Alexis Rohou 16 Nov '23

16 Nov '23

Hello, I'm playing around with the define axis command, and noticed that in the documentation the link to "plane-spec" does not lead to anything that defines how to specify a plane (help:user/commands/atomspec.html#othermodels). Or at least, I can't see it. The link to "point-spec" does take me to an informative page (help:user/commands/pointspec.html#point). Is the syntax for specifying a plane defined elsewhere? This is with 1.6.1. Cheers, Alexis

2 2

extracting cryoem density
by Dmitry Semchonok 16 Nov '23

16 Nov '23

Dear colleagues, I have a cryo-EM map with different subunits and models for each unit. Is there a way to extract the cryo-EM density for each unit of this map? The units are pretty numerous😊 Thank you. Kind regards, Dmitry

3 2

Calculating solvent accessible surface area for all residues in a protein?
by Altobelli, Chad 15 Nov '23

15 Nov '23

Hi! Is there a way to calculate the solvent accessible surface area (SASA) for every residue in a protein (5FTL) and output the result to a text file? I am trying to rank order residues by their accessibility. I know I can use the command line to calculate one residue at a time but it's laborious. Is there a way to automate the process or a GUI shortcut? Thanks! Chad

2 2

ChimeraX-1.7.dev202311052311-Ramachandran Plots
by Berkay Ekren 15 Nov '23

15 Nov '23

Hello, FIrst of all, I have been using Chimera for 3-4 years, now, and I would like to thank you for your efforts in the development of Chimera and ChimeraX. Recently, I decided to move to ChimeraX, and stay updated by using the bleeding edge daily version. However, I haven't been able to see the Ramachandran Plots option in either the Model Panel or the Tools section of ChimeraX. Is the Ramachandran Plots function removed from the program? Or is it just that I haven't looked at the correct path. This is a Linux installation in Debian 12 (used Ubuntu 22.04 deb package) It would be great if you could direct me to the right direction. Thank you in advance, I am looking forward to hearing from you at your earliest convenience. --Berkay Y. Ekren PhD candidate in Biostatistics and Bioinformatics

2 1

substitute nonstandard residue
by Dmitry Semchonok 15 Nov '23

15 Nov '23

Dear colleagues, I have a short question - how to substitute nonstandard residue with other ChimeraX. My task is to substitute GTP for GSP. The one may use swapaa, right? Could anyone drop the usage for nonstandard residue? Many thanks. Sincerely, Dmitry

2 1

ChimeraX on Apple M1
by Dennis Dannecker 15 Nov '23

15 Nov '23

Hello, I have a question regarding running ChimeraX on Apple's M1 chip. About two years ago (Nov 2, 2021), there was a post by Tom announcing the development of a version of ChimeraX that would run natively on Apple M1 instead of emulting for the Intel processor. Looking in the download section, I see such a native version is now regularly released. However, I am wondering what is the differen between the "macOS M1 or M2" and "macOS". While the former is only for M1 and M2, the latter on is for M1, M2, and Intel Macs, this one is also quite larger in size. If one is working on a macOS M1 (or M2) machine, is it correct to go for the "macOS M1 or M2"? Would that correspond to natively running ChimeraX and provide the best possible performance, or should one always go for the "macOS" release? I am currently updating my hardware, and since I am working quite a bit with ChimeraX, I would like to also inform my decisions based on the available ChimeraX releases. Thank you very much. Best regards Dennis Dennis Dannecker Master Student of Biochemistry Department of Chemistry Faculty of Mathematics and Natural Sciences University of Cologne Albertus-Magnus-Platz 50923 Cologne, Germany

2 2

Not able to see Glycines in stick form
by Firdous Tarique 14 Nov '23

14 Nov '23

Hi everyone In ChimeraX I am not able to show Gly simultaneously as a stick and cartoon. If I am trying to show Gly as a stick then the cartoon line breaks up at this position. And this is for any of the structures if you see. By showing a cartoon and stick together, the sticks for all amino acids show up except for Gly where it remains in the cartoon (you can try that). My aim is to show the thioester bond between Gly and Cys of two chains which I am able to create in Coot through Molecule Link but not able to see in ChimeraX. The moment I am trying to show Gly in stick form at this position it breaks the cartoon. I realised that this is for all the Glycines in the structure. Showing stick and cartoon together shows all amino acids in the stick except Glycine. (However this is not the case in Pymol and Chimera). Do you know any tricks to fix that in ChimeraX? Best Firdous

2 2

(no subject)
by Enrico Martinez 14 Nov '23

14 Nov '23

Dear Chimera-X users! I am trying to record md trajectory loaded in the chimera as

1 0

Re: [ccpem] Making thioester bond in Chimera/ChimeraX
by Elaine Meng 13 Nov '23

13 Nov '23

Hi Firdous, No trick, it is an option of cartoon (on by default) to prevent showing backbone atoms at the same time. Glycine only has backbone atoms (no sidechain). If you really want to show cartoon and backbone atoms at the same, use cartoon suppress false This is explained in the "cartoon" or "ribbon" command help. Just type command "help cartoon" to see your downloaded copy of the help page, or see the copy on our website here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> The full name of the option is "suppressBackboneDisplay" but you can shorten all options in commands as long as there is no other option that starts with the same letters. Actually Chimera ribbon also hides backbone atoms by default, although you can allow showing both at the same time with the Chimera "ribbackbone" command. The best address to use for ChimeraX questions is the chimerax-users one that I CC'd on this message, unless you are including data that must be kept private. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 13, 2023, at 2:59 PM, Firdous Tarique <kahkashantarique(a)gmail.com> wrote: > > Hi Elaine > > Now I know where the problem is. In ChimeraX I am not able to show Gly simultaneously as a stick and cartoon. If I am trying to show Gly as a stick then the cartoon line breaks up at this position. And this is for any structure if you see. By showing a cartoon and stick together, the sticks for all amino acids show up except for Gly where it remains in the cartoon (you can try that). However this is not the case in Pymol and Chimera. Do you know any tricks to fix that in ChimeraX? > > Best > > Firdous > > On Thu, Nov 9, 2023 at 6:11 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hello Firdous, > Probably the problem is that mol A and mol B are two different models. You can't add a bond in Chimera or ChimeraX until after combining them into one model first. > > ChimeraX combine command: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> > > ChimeraX bond command or Build Structure tool, Adjust Bonds section: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html> > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> > > For the best chance of getting an answer to a question about ChimeraX, please use the chimerax-users(a)cgl.ucsf.edu address: > <https://rbvi.ucsf.edu/chimerax/docs/contact.html> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > From: Collaborative Computational Project in Electron cryo-Microscopy <CCPEM(a)JISCMAIL.AC.UK> on behalf of Firdous Tarique <kahkashantarique(a)GMAIL.COM> > > Date: Thursday, November 9, 2023 at 12:27 PM > > To: CCPEM(a)JISCMAIL.AC.UK <CCPEM(a)JISCMAIL.AC.UK> > > Subject: [ccpem] Making thioester bond in Chimera/ChimeraX > > > > Hi > > > > Does anybody know how to make thioester bonds in Chimera or ChimeraX ? > > > > I am unable to make a bond between Cys321 in mol A with Gly1 in mol B (S-glycyl-L-cysteine) using Chimera or ChimeraX. > > > > I tried Isolde in ChimeraX and Build Structure in Chimera to make a bond between selected atoms but so far have been unsuccessful. I don't know if I am missing something. > > > > Any help would be appreciated. > > > > Thanks > > > > Firdous > > > > To unsubscribe from the CCPEM list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1 > > >

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projecting full model from monomer
by Dmitry Semchonok 13 Nov '23

13 Nov '23

Dear colleagues, I have a monomer with biomt information that describes the full model. To see the full model, I use the command sym when opening the monomer in Chimera. Could you please prompt the correspondent command in ChimeraX to project the complete model in ChimeraX based on the information stored in the monomer? Thank you Kind regards, Dmitry

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ChimeraX trial license
by Jang,Chang Woon,US-St. Louis 12 Nov '23

12 Nov '23

Dera UCSF ChimeraX Team, My name is Chang Woon Jang working for Nestle Purina. I am interested in ChimeraX for a molecular modeling project. Could I use a trial license for a month before buying the commercial license? Thanks, Chang Woon Jang

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updating ChimeraX for rc/daily build with Isolde
by Dmitry Semchonok 11 Nov '23

11 Nov '23

Dear colleagues, I would like to update ChimeraX to rc version or daily build. Trying to install Isolde / Clipper delivered me the following error (either via the command line within ChimeraX, or via the ChimeraX update button) Clipper toolshed install C:/Users/Dmitry/Downloads/ChimeraX_Clipper-0.22.1-cp311-cp311-win_amd64.whl ERROR: Could not find a version that satisfies the requirement ChimeraX-Core<1.8,>=1.7.dev202306142048 (from chimerax-clipper) (from versions: none) ERROR: No matching distribution found for ChimeraX-Core<1.8,>=1.7.dev202306142048 ISOLDE toolshed install C:/Users/Dmitry/Downloads/ChimeraX_ISOLDE-1.7.dev0-cp311-cp311-win_amd64.whl ERROR: Could not find a version that satisfies the requirement ChimeraX-Core<1.8,>=1.7.dev202306142048 (from chimerax-isolde) (from versions: none) ERROR: No matching distribution found for ChimeraX-Core<1.8,>=1.7.dev202306142048 Is it possible to install Isolde/clipper with rc/daily version? If yes, how to fix the error? Thank you. Kind regards, Dmitry

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Zooming in and out in ChimeraX
by Dale Calleja 09 Nov '23

09 Nov '23

Hello, I am currently learning to use ChimeraX (v1.6.1) and I am having issues with my scroll wheel. I notice when I first open the software using the scroll wheel on my mouse will zoom in and out of the structure but, after some time it simply stops working and the scroll wheel does nothing. Is this a button I am accidentally pressing or have I discovered a bug? It doesn’t seem to have any pattern, I am just clicking around changing the display of my protein. Thanks! Dale. Dale Calleja PhD Student, Komander Lab Ubiquitin Signalling Division WEHI 1G Royal Parade Parkville VIC 3052 Australia Email calleja.d(a)wehi.edu.au<mailto:calleja.d@wehi.edu.au> [WEHI Logo] Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville Victoria 3052 Australia www.wehi.edu.au<https://wehi.edu.au> Twitter<https://twitter.com/WEHI_research> | Facebook<https://www.facebook.com/WEHIresearch/> | Instagram<https://www.instagram.com/wehi_research> | Youtube<https://www.youtube.com/user/WEHImovies> | LinkedIn<https://www.linkedin.com/company/wehi_research> WEHI acknowledges the Wurundjeri people of the Kulin Nation as the traditional owners of the land where our campuses are located and the continuing connection to country and community. Private and confidential The content of this e-mail and any attachments may be private and confidential, intended only for use of the individual or entity named. If you are not the intended recipient of this message you must not read, forward, print, copy, disclose, use or store in any way the information this e-mail or any attachment contains. If you are not the intended recipient, please notify the sender immediately and delete or destroy all copies of this e-mail and any attachment.

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ui mousemode right when in ISOLDE
by Alexis Rohou 09 Nov '23

09 Nov '23

Hi there, Wondering if anyone else gets this behavior: When ISOLDE is running, setting the right mouse click to translate selected atoms does NOT associate shift-right-click with rotating selected atoms; instead, shift-right click does a zoom. In addition, if I try to force it by issuing the two commands below, the shift right click still isn't a rotate selected atom; instead, it does a translate selected atoms. ui mousemode right "translate selected atoms" ui mousemode shift right "rotate selected atoms" My workaround is to use alt-right for rotating instead. That does work: ui mousemode right "translate selected atoms" ui mousemode alt right "rotate selected atoms" This is with ChimeraX 1.6.1, but I'm pretty sure I noticed this behavior in earlier versions also. Tristan recently posted a screen capture where it's clear he doesn't have this problem, but he's on Windows and I'm on Mac, so I wonder whether that might have something to do with it. Any ideas? Cheers, Alexis

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how to build N-linked glycans
by Alexis Rohou 09 Nov '23

09 Nov '23

Hi there, How would you recommend I go about building an N-linked glycan chain off of an ASN in an existing model using ChimeraX or ISOLDE? Is there documentation on this somewhere? Cheers, Alexis

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