- ChimeraX-users - RBVI Mailing Lists

Is there a way to reset memory?
by David Flesher 21 Feb '24

21 Feb '24

Hi ChimeraX team, I've been writing a script to run within ChimeraX and, as I continue to run the script, the system memory quickly fills up to my system maximum (32 GB). Is there a way to refresh/dump the memory within ChimeraX? My script creates markers but deletes them with every iteration, which I thought would keep memory in check. Please let me know if you have any advice, thank you! Best regards, :David

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Saving volumes from volume morphs
by y.zeng＠victorchang.edu.au 21 Feb '24

21 Feb '24

Hi, I wanted to ask if there is a way to save each frame of a volume morph through the command line, or if a feature like this could be added? I would like to use each frame of the volume morph series (as .mrc) to export into an external program, but the only way I've found at the moment is to manually change each frame in the morph slider then save that frame. It doesn't appear there is the same coordset slider functionality of the volume morph slider for atomic models, which would be really handy in my situation if the morph has lots of steps. Many thanks Jack

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Image as the background
by Enrico Martinez 21 Feb '24

21 Feb '24

Dear ChimeraX users! I'm wondering if it's possible to set the custom image as the background in a Chimera-x session in the same way as in the Chimera? If it's not possible, will this feature be included in future versions of Chimera-X? Many thanks in advance Enrico

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Seeking Assistance with PyCharm Debugging Configuration
by himalgodage2759＠gmail.com 20 Feb '24

20 Feb '24

Dear ChimeraX Dev Team, I'm Himal Godage, and I am currently in the process of developing a bundle for ChimeraX software. I have been thoroughly following the provided documentation, successfully completing the steps related to setting up a ChimeraX development environment, obtaining the code, and compiling ChimeraX. However, I have encountered a challenge in the IDEs, Debugging, and Profiling section, specifically within PyCharm. Following the provided steps, I am instructed to: 1. Create a new Run/Debug Configuration. 2. Set the script path field to point at a module. 3. Set the module to “chimerax.core”. 4. Set the Python interpreter to ChimeraX’s internal Python. 5. Uncheck “Add content roots to PYTHONPATH”. 6. Uncheck “Add source roots to PYTHONPATH”. While attempting to follow these instructions, I encountered difficulty in locating the "chimerax.core" module. Unfortunately, the provided directory structure or module seems to be difficult to find in my current project. However there is a module named core in the following path. ChimeraX > src > bundles > core I am reaching out to seek your guidance on resolving this issue. Could you please provide insights on how I can locate or create the necessary "chimerax.core" module or suggest an alternative approach to address this problem? Thank you in advance for your time and support. Best regards, Himal Godage himalgodage2759(a)gmail.com

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Ending a beta strand depiction
by Noam Prywes 20 Feb '24

20 Feb '24

Hi, I'm trying to make an image where I've clipped a bunch of beta strands that together form a barrel. I want to have them end simply as arrows rather than continuing to show that small remaining tube of the subsequent loop. Any advice? Thanks! Noam Prywes UC Berkeley [image: Screenshot 2024-02-20 at 8.09.47 AM.png]

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BUG: Individual change ball&stick does not work
by Christian Tüting 19 Feb '24

19 Feb '24

Dear ChimeraX dev team, I found an issue with the styling of the ball&stick representation in ChimeraX. Here is a code snipplet to see the issue: # load a random model and show two residues open 7ott hide cartoons show #1:283-284 atoms style #1:283-284 ball # this worked size #1:283 stickRadius 0.1 size #1:284 stickRadius 0.25 # this does not work size #1:283 ballScale 0.4 size #1:284 ballScale 0.1 The ballScale value is not applied on the selection like the stickRadius, but is always applied globally. I am running the latest daily build (1.8.dev202402162121 (2024-02-16 21:21:18 UTC)) on MacOS. Best Christian

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Surface color by homology
by Pedro Bule 17 Feb '24

17 Feb '24

Hello, I am trying to color the surface of my model according to sequence conservation. I opened the MSA, associated the proper sequence with the chain I wish to color, and then used the command "color byattr seq_conservation". But this results in the colors not blending at the surface, which is not very pleasant looking. Is there a way to make the transitions between adjacent colors smoother, similar to when we color the surface, for e.g., by electrostatic potential? In legacy chimera I used to follow the "Structure... Render by Conservation" in the Multalign Viewer and then choose the attribute mavConservation, which used to do the trick Thanks in advance! Pedro Bule -- *Pedro Bule* *Assistant Professor* GLYCOBIOLOGY AND STRUCTURAL ENZYMOLOGY LAB *P:* (+351) 21 365 28 84 // 431379 | pedrobule(a)fmv.ulisboa.pt <email(a)fmv.ulisboa.pt> *Centro de Investigação Interdisciplinar em Sanidade Animal* Faculdade de Medicina Veterinária Av. Universidade Técnica | 1300-477 Lisboa | PORTUGAL

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Question about aligning sequence to structure
by Rebekah Dyer 16 Feb '24

16 Feb '24

Hello, I'm wondering if there's a way to do the following with ChimeraX: 1. Open structure with associated sequence (seqA) 2. Open a separate sequence file (seqB) with no associated structure 3. Align seqB to seqA 4. Color residues on structure of seqA protein by conservation between seqA and B I've managed to complete steps 1 and 2, but am stuck on step 3. Any help or advice would be greatly appreciated! Best, Rebekah Dyer, Ph.D. (she/her) Staff Enzyme Scientist | Dexcom<https://www.dexcom.com/en-us> 6350 Sequence Dr. | San Diego, CA, 92121

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Swissdock
by Gabriel López Velázquez 14 Feb '24

14 Feb '24

What to do if ChimeraX software doesn't recognise the .chimerax file downloaded from SwissDock after docking? Gabriel

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Size of side chains
by Binh Nguyen 14 Feb '24

14 Feb '24

Dear all, Is there a command to make the side chains smaller? Here is what I got: [cid:de6b4361-2537-4331-beb5-0571611bebe4] And I wish to have this using chimeraX: [cid:4dc1c6e4-62b3-4eb5-b350-227da1b7821c] Thanks, B ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Save docked tool size?
by Guillaume Gaullier 14 Feb '24

14 Feb '24

Hello chimerax-users, I recently started using ChimeraX in more custom ways for specific analyses, for which I need several tools displayed at once. I need some docked and others floating. So the "Save tool position" option is very helpful. However, it saves window size only for floating tools, not docked ones, so I have to resize the docked tools at every restart (their position is saved correctly, but not their size relative to the main ChimeraX window). This happens for the model panel and log, that I have docked to the right of the 3D display: they systematically start much wider than I want (and than I resized them to last time I started ChimeraX). This doesn't happen for a custom button panel that I have docked to the right of the toolbar (but maybe because the command file generating the panel sets a fixed size explicitly?). I have not checked whether this happens with other tools. Is this normal behavior? If so, is there any way I can make docked tools remember not only their position but also their size? A quick search in the documentation didn't answer this question. Thank you, 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

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Feature request; sort by last time file was modified in save window
by m.c.feasey2＠newcastle.ac.uk 12 Feb '24

12 Feb '24

The content of this message was lost. It was probably cross-posted to multiple lists and previously handled on another list.

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Chimera Script
by Dixson, Jamie 12 Feb '24

12 Feb '24

Hello, I would like to use the Matchmaker comparison in ChimeraX (specifically the 'across all' RMSD value given) to compare 10,000+ structures so I would like to incorporate it into a python script in a jupyter notebook. I am very familiar with scripting with python in jupyter notebooks but I am not as familiar with getting two scripts to work together as appears to be needed to use matchmaker in an existing jupyter script. The script I am attempting to use is found below. I wrote it following some of the guidance in your documentation. ``` #Chimera Command Line import chimera import os from chimera import runCommand as rc # use 'rc' as shorthand for runCommand from chimera import replyobj # for emitting status messages file1='C:/Users/jamie/Downloads/temppdb1.pdb' file2='C:/Users/jamie/Downloads/temppdb2.pdb' structure1=rc("open " + file1) structure2=rc("open " + file2) rc("mmaker structure1 structure2") ``` I get the error 'No chimera module' I try to install chimera using 'pip install chimera' and it won't install. Can you offer any guidance on getting this to work? Best, Jamie Dixson

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Automatisation of the movie record / encode
by Enrico Martinez 11 Feb '24

11 Feb '24

Dear Chimera-X users! Typically when I load multi model pdb using open coordset true I may record my movie automatically using the context menu. I need to script this process selecting the resolution and the quality of the encoding using movie record size 3840,2160 supersample 3 movie encode format h264 quality highest output ./my_movie.mp4 The only problem is that when I type the first command it asks me to "play" and then "stop" the pdb ensemble for the number of frames which should be present in the resulting video. Is it possible to define in the scipr that the movie should take the selected number of frames in the selected range and then automatically start to encode the movie ? Many thanks in advance Enrico

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Setting transparency for multi-frame PDB
by Enrico Martinez 09 Feb '24

09 Feb '24

Dear ChimeraX users! I am working on visualization of protein-ligand complex from MD trajectory loaded as multiframe pdb via open coordset true Here is my script: #coloring ligand options color ligand & C gold style ligand sphere #transparency surface protein color byattribute kdh protein target rs palette sandybrown:coral:orangered novalue gray transparency protein 5 surfaces select zone ligand 4 protein transparency sel 55 surface The problem is only in the transparency which could be set only on the first frame but then disappears when I browse movie. How could I modify my scipr to keep the transparency on all frames ? Many thanks in advance ! Enrico

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Surface representation for small compounds
by Enrico Martinez 09 Feb '24

09 Feb '24

Dear ChimeraX users I am also experimenting on the representation of the surfaces of small compounds surface ligand gridSpacing 0.5 probeRadius 1.2 color ligand white target s transparency 90 This creates a relatively large transparent surface around the small compound. How would it be possible to reduce the volume of the surface ? Also I did not understand how to change the style of the surface among dot/mesh etc since adding style dot did not work. I would appreciate any further creative examples of how to change the representation of a small compound in the case when I need to make it more "coarse-graining" , hiding some precise details of the structure ? Many thanks in advance ! Enrico

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Colour patterns for ligand atoms
by Enrico Martinez 09 Feb '24

09 Feb '24

Dear ChimeraX users ! I am experimenting with some unusual coloring of the ligand atoms represented as balls and sticks. the following commands color ligand atoms: size ligand atomRadius +3.0 color ligand & C gold target a color ligand goldenrod target a However, the following command does not work w/o any error message rainbow ligand & C palette cornflowerblue:red:gold target a I've also tried without any success. style ligand ball ringFill off rainbow ligand & C palette cornflowerblue:red:gold target f Any additional suggestions e.g. for the situation when I would like to alternate the colors for the ligand atoms in a regular fashion : e.g. the first atom white, the first black, the third white, the forth black etc ? Many thanks in advance ! Cheers Enrico

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Llama2 cannot be used as an alternative to the mailing list
by Pranav Shah 08 Feb '24

08 Feb '24

As the subject states. (see attached image for context) So thank you Elaine (and rest of the CX team) for your tireless and infinite capacity to support users! :) Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Fourier transformation of the 3D volume
by Dmitry Semchonok 08 Feb '24

08 Feb '24

Dear colleagues, How to get the Fourier transformation of the 3D volume? thank you. Kind regards, Dmitry

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Re: ChimeraX: AlphaFold data saving help
by Tom Goddard 06 Feb '24

06 Feb '24

Hi Tony, Good. I didn't see the sleep issue mentioned in our ChimeraX documentation. We'll add that. Tom > On Feb 6, 2024, at 2:35 PM, Anthony Newcombe <ant.newcombe(a)gmail.com> wrote: > > Ah ok thanks Tom! > > My PC does go into sleep mode, I'll turn this off and try again! > > Many thanks for the help > > Best wishes > > Tony > > Anthony Newcombe > Brook Lodge > Lisnacunna > Ballinascarthy > Clonakilty > Cork > > On Tue, Feb 6, 2024 at 10:25 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Tony, >> >> If you let your computer sleep when the ChimeraX AlphaFold job is run on Google Colab it will probably lose the results. Google intends Colab to be for interactive use. So I suggest setting your computer not to sleep when running a prediction. There is more discussion of AlphaFold prediction not downloading on the ChimeraX mailing list >> >> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu… >> >> including how you can get the results if Google Colab has not closed the session and deleted them (happens within a few hours). >> >> Tom >> >> >>> On Feb 6, 2024, at 5:57 AM, Anthony Newcombe via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hello ChimeraX team >>> >>> I am evaluating ChimeraX (non-commercial use) but have an issue you may be able to help with. When I run a structure prediction: >>> >>> Tools > structure prediction > AlphaFold >>> >>> I enter two primary sequences and hit ‘predict’ >>> >>> The simulation completes, but nothing opens in ChimeraX, also there is no data saved in the location below. I have tried alternative locations, but no data is saved >>> >>> ~/Downloads/ChimeraX/AlphaFold/prediction_[N] >>> >>> Do you know how I obtain saved predicted results ChimeraX? Do I need a paid service for this? >>> >>> Many thanks >>> >>> Tony >>> >>> Anthony Newcombe >>> Brook Lodge >>> Lisnacunna >>> Ballinascarthy >>> Clonakilty >>> Cork >>> _______________________________________________ >>> 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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ChimeraX AlphaFold
by Nadine Hellmold 06 Feb '24

06 Feb '24

Hi dear support team, I am so happy to use AlphaFold directly in ChimeraX and it work's so smooth! Thanks a lot for it. I was wondering what the feature "Use pdb templates when predicting structures" exactly means? I understood it like during the prediction up to 4 templates from pdb database can be used. I used the option for one prediction, for a protein complex prediction with five proteins, and found way more than four templates used for each protein. If the option is switched off, what is used as a template then? Bests Nadine -- NadineHellmold PhD student Department of Environmental Biotechnology | Helmholtz Centre for Environmental Research - UFZ 0341 235-1766 <tel:0341 235-1766> nadine.hellmold(a)ufz.de <mailto:nadine.hellmold@ufz.de> PermoserstraCe 15, 04318 Leipzig, Germany <https://www.hubspot.de/email-signature-generator?utm_source=create-signature>

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ChimeraX: AlphaFold data saving help
by Anthony Newcombe 06 Feb '24

06 Feb '24

Hello ChimeraX team I am evaluating ChimeraX (non-commercial use) but have an issue you may be able to help with. When I run a structure prediction: Tools > structure prediction > AlphaFold I enter two primary sequences and hit ‘predict’ The simulation completes, but nothing opens in ChimeraX, also there is no data saved in the location below. I have tried alternative locations, but no data is saved ~/Downloads/ChimeraX/AlphaFold/prediction_[N] Do you know how I obtain saved predicted results ChimeraX? Do I need a paid service for this? Many thanks Tony Anthony Newcombe Brook Lodge Lisnacunna Ballinascarthy Clonakilty Cork

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DNA/RNA style in ChimeraX
by Woo-Ri Shin 06 Feb '24

06 Feb '24

Hi I have a question about making images for protein-DNA(or RNA) complex structures. I want to make the round shape of DNA (or RNA) backbone using "nucrib" command which is provided on the web ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cartoon.html) But this command doesn't work. I have the docking structure including RNA of chain A and protein of chain B. So then I modified the command like this: *alias nucrib cartoon style /A xsect oval width 1.6 thick 1.6* This command doesn't work and still initial cartoon style. Could you check this problem? [image: image.png] Thank you Best, Woo-Ri Shin -- *Woo-Ri Shin, Ph.D.* Department of Bioengineering University of Pennsylvania E-mail: wr1203(a)seas.upenn.edu Phone: +1 (267)213-2572 ᐧ

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Coloring maps based on segmentation
by M. Elizabeth Stroupe 05 Feb '24

05 Feb '24

Hi, I am having some trouble coloring my map based on segmentation. It used to be straightforward from the “Regions” menu of the segmentation tool, but now I am getting an error "TypeError: unsupported operand type(s) for *: 'float' and 'NoneType' File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/segger/regions.py", line 1884, in color_surface_pieces xyz = v - offset*n” I also tried to do it by line command but I confess I am not sure what to put for “seg-map”. Thank you for your help, Beth

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Information storage
by Cygler, Miroslaw 05 Feb '24

05 Feb '24

Hi, When ChimeraX opens, it restores list of commands used in previous session(s) and the files/sessions there were accessed previously (history). Where is this data stored on the computer? How can I preload specific settings to take effect on ChimeraX opening? Thanks, Mirek

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ChimeraX on new Apple cpus
by Enrico Martinez 05 Feb '24

05 Feb '24

Dear ChimeraX users! I am considering purchasing one of the recent macbook pro equipped with the modern M2 or M3 apple chips. Assuming that presently I am using the 2015 model equipped with the i7 4 core cpu and discrete radeon gpu, what should be expected increase of the performance in the case of recording of MD movies with ChimeraX using the performance of a new mac ?? Many thanks in advance Enrico

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Save PDB relative to map - does not store relative postion
by Dennis Dannecker 02 Feb '24

02 Feb '24

Hello, I am running into an issue with saving pdb coordinates and their relative postioning. I am fitting an atomic model into a map model, explicitly the atomic model is rotated and translated into the map using fitmap (local optimization, rigid body fitting). Once the fit is complete, the atomic model is saved as a PDB file with the checkmark set on "Save relative to model...", here I have chosen the map the atomic model has just been fit to. This is, I think, in accordance with what is adviced in the doc of the "Fit in Map" Tool. However, when I reopen said atomic model and map in a new chimerax session (loading the map and loading the pdb file just saved relative to this map), none of the rotational and translational information is kept and the map and atomic model are in no meaning full spatial relationship. I wanted to use this procedure to prepare for cryofit and/or real space refinement in phenix, so I would like to use map and pdb for another software. As is mentioned in the doc of the "Fit in Map" Tool, volume files generally do not store rotation, thus the pdb file should be chosen to capture the rotational and translation information. Am I understanding something wrongly here or how come that the postioning is completely off when I reload map and model? Thank you for your help. 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

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Display volume default threshold level
by Chenwei Zhang 02 Feb '24

02 Feb '24

Dear UCSF ChimeraX developers, I am Chenwei Zhang, a PhD student from UBC, Canada. I am currently using ChimeraX for cryoEM density map visualization, which did a really nice job. There's one question I would like to seek answers from you. When I show a density map in ChimeraX GUI, it show automatically show a threshold level. Here's a quick example when I open emd_6272.map file: _Opened emd_6272.map as #1, grid size 108,108,108, pixel 1.02, shown at level 0.0555, step 1, values float32_ May I ask how does ChimeraX get this threshold? Or more generally, how does ChimeraX calculate the density values to get this final threshold value? Is there any command I could use in ChimeraX to extract this value? I tried to find answers in your documentation but failed so I am writing this email for help. Thank you in advance and look forward to your reply. Best, Chenwei

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Using GPU in chimerax
by Sharif, Omar 01 Feb '24

01 Feb '24

Hello, I am using Chimerax with a tool called DeepSSETracer, a model that performs segmentation on the secondary structure of 3d cryo density maps. I need GPUs and CUDA enabled to test the tool. When I run the model, I have a message in the log that says Cuda is not available although I am running on a machine where relevant Nvidia GPU drivers and Cuda are already installed and working properly. I am attaching the screenshot [cid:d821ceae-9b2c-4a88-a7ba-c45b2935bee2] Is there any way to enable GPU usage within the ChimeraX? Is there any way to check if ChimeraX is using GPU and CUDA? I will be waiting for your reply. Thanks in advance, Omar Omar Sharif Ph.D. student Department of Computer Science Old Dominion University Email: osharif(a)cs.odu.edu https://odu.zoom.us/my/omarsharif786

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Center atom
by Cygler, Miroslaw 31 Jan '24

31 Jan '24

Hi, I just started using ChimeraX and am confronted with how to do a simple task, namely, to placer a specific atom at the centre of the screen. What is the replacement for the command “centre” in Chimera? Thanks, Mirek

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opening the session made with the new ChimeraX version using old ChimeraX
by Dmitry Semchonok 31 Jan '24

31 Jan '24

Dear colleagues, I made a session (cxs) in the newest ChimeraX. It contains the models only. How can I open it in the older ChimeraX version? Maybe I can save the session in a different format to be able to open with the older version? Unfortunately, I cannot update the older version on one PC. Thank you. Kind regards, Dmitry

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transparency around the model only
by Dmitry Semchonok 31 Jan '24

31 Jan '24

Dear colleagues, I have a cryo-EM 3D map and model. A model is fitted for only part of my cryo-EM map. Is there a command to make the map transparent only where the model is fitted in? Thank you. Kind regards, Dmitry

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Antivirus software warns about "Trojan.Win32.Diple" in 1.7.1 ChimeraX executable
by thomas.coudrat＠gmail.com 31 Jan '24

31 Jan '24

Hi ChimeraX list, When trying to install ChimeraX 1.7.1 Windows (md5: c79878497cfa2c1e0944e732ea4adc21) I get a warning from my antivirus software. See the description here: https://www.virustotal.com/gui/file/cc9b4af4e1a04fc647d082e04f60c111c7aeed1… In case the link doesn't work, it says that "Ikarus" is warning about "Trojan.Win32.Diple", while passing the checks with several other antivirus software. (I've seen a similar thread in the archive but it was from last year, therefore this one might be different) Kind regards, Thomas

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rrdistmaps in chimerax?
by Francisco Murphy Pérez 30 Jan '24

30 Jan '24

I just learned about this program called RRDistMaps https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410660/ in UCSF chimera. Is there something similar in chimeraX? Thanks

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Modeller using more than 1 template in Chimera Modeller
by Vladimir Saudek 29 Jan '24

29 Jan '24

Hello, Is it possible to model 3D structure within Chimera using several complementary pdb templates at once? This is possible in the stand alone Modeller but I was unable to find a tutorial/manual instruction how to do it in Chimera. Thank you Vladimir

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mixed backbone/sidechain display for N-terminal residue
by hirbond＠utexas.edu 28 Jan '24

28 Jan '24

Hi everyone, I've been working on a protein display that I want to explicitly show the sidechain and backbone atoms of the N terminal residue. The problem is with the cartoon representation. For the N terminal, the cartoon rep goes beyond the CA atom and sticks out. Any tip on how I can change it? I thought of eliminating the pseudobond representation for the CA atom so that the cartoon representation doesn't happen between C and CA but it did not work for me. Thanks!

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Problem with Chimerax on Ubuntu 20.04
by svle＠tiscali.it 26 Jan '24

26 Jan '24

Hi, I've installed Chimerax 1.7.1 using the .deb. When launching the application from the icon It appears the Chimerax window along with another error panel and after one or two seconds these are closed. If I call Chimerax from a shell I receive the following: $ chimerax NOTE: available bundle cache has not been initialized yet [48347:48390:0126/183239.131894:ERROR:skia_output_surface_impl.cc(927)] surface_size=1224x615 format=6 color_type=4 backend_format.isValid()=0 backend_format.backend()=5 backend_format.asGLFormat()=0 backend_format.asVkFormat()=0 backend_format.asVkFormat() vk_format=0 surface_origin=1 willGlFBO0=0 Segmentation fault (core dumped) If this can be useful on my laptop: $ uname -a Linux xxxx-Lenovo-IdeaPad-S340-15API 5.4.0-74-generic #83-Ubuntu SMP Sat May 8 02:35:39 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux $ glxinfo -B name of display: :0 display: :0 screen: 0 direct rendering: Yes Extended renderer info (GLX_MESA_query_renderer): Vendor: AMD (0x1002) Device: AMD RAVEN (DRM 3.40.0, 5.4.0-74-generic, LLVM 11.0.1) (0x15d8) Version: 20.3.4 Accelerated: yes Video memory: 2048MB Unified memory: no Preferred profile: core (0x1) Max core profile version: 4.6 Max compat profile version: 4.6 Max GLES1 profile version: 1.1 Max GLES[23] profile version: 3.2 Memory info (GL_ATI_meminfo): VBO free memory - total: 866 MB, largest block: 866 MB VBO free aux. memory - total: 5689 MB, largest block: 5689 MB Texture free memory - total: 866 MB, largest block: 866 MB Texture free aux. memory - total: 5689 MB, largest block: 5689 MB Renderbuffer free memory - total: 866 MB, largest block: 866 MB Renderbuffer free aux. memory - total: 5689 MB, largest block: 5689 MB Memory info (GL_NVX_gpu_memory_info): Dedicated video memory: 2048 MB Total available memory: 7928 MB Currently available dedicated video memory: 866 MB OpenGL vendor string: AMD OpenGL renderer string: AMD RAVEN (DRM 3.40.0, 5.4.0-74-generic, LLVM 11.0.1) OpenGL core profile version string: 4.6 (Core Profile) Mesa 20.3.4 OpenGL core profile shading language version string: 4.60 OpenGL core profile context flags: (none) OpenGL core profile profile mask: core profile OpenGL version string: 4.6 (Compatibility Profile) Mesa 20.3.4 OpenGL shading language version string: 4.60 OpenGL context flags: (none) OpenGL profile mask: compatibility profile OpenGL ES profile version string: OpenGL ES 3.2 Mesa 20.3.4 OpenGL ES profile shading language version string: OpenGL ES GLSL ES 3.20 The same problem also with Chimerax 1.7.0 but not 1.6. Thanks. Saverio

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CA atoms connected by tether when trying to show sidechains only in a model
by Samuel Haysom 25 Jan '24

25 Jan '24

Hello, I am trying to show only sidechains in one model, so I can compare rotamers with another model where I am displaying cartoon and sidechains. However, when I display sidechains using the sidechain selector (e.g. "show #1 & sidechain") the CA atoms become linked by tethers. [cid:image001.png@01DA4F98.8C977390] How can I suppress this display? I can see its possible to suppress tethers between cartoon helices and a sidechain in the same model but that doesn't seem to apply here as I'm not showing the cartoon at all in the models where the CA tethers are present. KR, Sam Samuel Haysom | Research Scientist | Biophysics Sosei Heptares | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Heptares Therapeutics Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

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Inquiry on Commercial Licensing for ChimeraX Plugin Development
by Jacky Chen 24 Jan '24

24 Jan '24

Dear Team ChimeraX, My name is Jacky Chen, and I am the sales representative at Oomii. Recently, we initiated a project aimed at developing an innovative ChimeraX plugin, specifically designed to enable interactive augmented reality features. To this end, Oomii has acquired two commercial licenses of ChimeraX in January 2024. As we progress, our intention is to offer the developed bundle for commercial sale to other users. However, upon reviewing the documentation available at: https://www.cgl.ucsf.edu/chimerax/docs/devel/writing_bundles.html, we noticed that it does not specify the licensing particulars for a bundle that utilizes both the ChimeraX API and proprietary code developed by Oomii. We are keen to ensure that our operations align with ChimeraX's licensing policies. Could you please provide guidance on the business rules that apply to the commercial distribution of such plugins? Additionally, if available, could you direct us to any precedent or contact information for companies that have navigated similar pathways? Your assistance in this matter is invaluable to us, and we eagerly await your insights. Thank you very much for your time and support. Warm regards, *Jacky Chen 陳志傑* *Sales Representative* * <https://oomii.com/>* *jackychen(a)oomii.com <jackychen(a)oomii.com>* *2F.-1, No.94, Baozhong Rd. Xindian Dist., New Taipei City, Taiwan 23144* *+886-2-8911-2347* <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> 乾淨無病毒。www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Feature question: "Worms" plots in "Render By Attribute"
by James Lingford 24 Jan '24

24 Jan '24

Dear ChimeraX team, I was wondering if ChimeraX v1.7+ has the function for rendering attributes by "Worms"? For example, rendering B-factors by the thickness of the backbone. I noticed that it's possible in legacy version of Chimera, which I have since installed and generated worm plots with: https://www.cgl.ucsf.edu/chimera/ImageGallery/framedpecworm.html Is this doable in the latest ChimeraX versions, however? Many thanks for any help you can provide, James -- *James Lingford* | Research Officer, Greening Lab Department of Microbiology, Monash Biomedicine Discovery Institute Monash University Google Scholar <https://scholar.google.com/citations?user=4KSRHTUAAAAJ&hl=en> | Website <https://www.jameslingford.com/>

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Re: [Chimera-users] Chimera X menu "View" vs. "Focus"
by Eric Pettersen 23 Jan '24

23 Jan '24

Hi Christian, We named it “View” instead of “Focus” because it issues a “view” command, but your points have merit — “Focus” is more evocative of what the action actually does, and is less confusable with hide/show, so after some discussion we have renamed the menu item to “Focus” and the change will be in the next daily build. The menu item item still issues/logs a “view” command to do its work. We are aware that the direct equivalent of the “Fetch By ID” dialog is missing in ChimeraX and we intend to add it. It’s just a matter of implementation priorities, so it could still be a little while — but it’s useful to know that it’s definitely missed, which will make it more likely to get worked on sooner. Also, there is a list specifically for ChimeraX user issues — chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>, (cc’ed here), which would be better to discuss ChimeraX topics on than chimera-users… --Eric Eric Pettersen UCSF Computer Graphics Lab > On Sep 25, 2023, at 12:47 AM, C. Klein via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera Team > > first of all, thank you very much for your important and good work on the Chimera software. > > Two comments: > > I did some recent work with Chimera X. The menu item "Focus" was changed to "View", which I find less suitable. The term "View" is often applied in other contexts, in particular if a certain residue should be shown vs. not shown. In contrast, "Focus" is not ambiguous, it is not related to showing vs. hiding certain parts of the molecular representation but exactly indicates what is done by the command. > > The direct pdb download from rcsb or whatever repository is a highly useful tool which is more difficult to access than it used to be. Ok I know it is there, I type "open xxxx" and I use the command line quite a lot anyway, but for others who start with the menus it does not appear to be accessible. Perhaps I also missed something, but then others may not find it as well. > > Thank you and best wishes > Christian Klein > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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Does ChimeraX work with tkinter?
by thlin＠oomii.com 22 Jan '24

22 Jan '24

I tried to use `tkinter` instead of `PyQt` but it does not work with ChimeraX 1.6 or 1.7's Python interpreter and the error message is shown below: ``` import _tkinter # If this fails your Python may not be configured for Tk ModuleNotFoundError: No module named '_tkinter' ``` One solution I've found was to `sudo apt install tk-dev` but it was required to`configure` and `make` ChimeraX's Python interpreter after. Does ChimeraX work with tkinter? If yes, then how to?

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Missing comand bar to open proteins
by Marina Contel 22 Jan '24

22 Jan '24

Hello, A few days ago, I was using ChimeraX and the command bar to open proteins disappeared. I have tried everything including uninstalling it and installing it again, and I have no clue how to solve it. I was wondering if you could give me some guidelines to get it back. That will be amazing because I need to start working with it as soon as possible because I have an assignment to hand this week. Thanks in advance! Kind regards, Marina

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[Inquire about the protein protein interaction results using chimeraX]
by ‍정혜연[학생](생명과학대학 유전생명공 학과) 22 Jan '24

22 Jan '24

Hi, I'm HyeYeon from KyungHee University. I am sending you an email because I have some questions while using ChimeraX. When I investigated the interaction between the two proteins using chimeraX, the results of the two runs were different even though they had the same sequence. One is the result from June of last year and the other is from January of this year. Did the PPI results change despite the same sequence as a result of the program update? I would appreciate it if you could check and reply. Thank you.

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Defining a variable that represents the number of models
by kkssy141＠gmail.com 20 Jan '24

20 Jan '24

Hello, Would it be possible to define a variable that represents the number of models? I want to make a chimerax script that aligns #1-#(N-1) to #N. For instance, if I have a script like this where N represents the number of models opened in ChimeraX and save it as test.cxc mm #1-#(N-1) to #N In bash, I can open my PDB files that are aligned to a crystal structure 1be9: chimerax *.pdb 1be9 test.cxc The number of models (N) will be a dynamic variable depending on how many PDB files I have. Thank you. Best, Siyoung ------------------ While writing, I figured the below would work. test.cxc: mm ~#1 to #1 In bash: chimerax 1be9 *.pdb test.cxc But I still want to ask this question to know whether it is possible to retrieve the number of models opened and set this to a variable in ChimeraX. Thanks.

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Colouring clipping plane
by GOVAERTS Cédric 20 Jan '24

20 Jan '24

Hi ChimeraX team. I’m trying to get an image of a protein whose surface is colored by electrostatic properties but clipped halfway. I would like the clipping plane to be white, not red/blue according to the electrostativ properties of the residues insides the protein. However, I don’t’ seem to be able to do that. -If I color everything white and then click on Molecular-Display “electrostatic”, the clipping plane also gets the electrostatic coloring [Graphical user interface Description automatically generated] -If I color everything white and then click on Molecular-Display “hydrophobic” or “rainbow” it works, the clipping plane remains white. [cid:image002.png@01D94092.6E8A2390] Can you help me getting the white clipping plane with electrostatic surface ? Thanks a bunch Cedric — Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

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Option to convert shape to map?
by Oliver Clarke 19 Jan '24

19 Jan '24

Hi, Would it be possible in a future release to add an option to the "shape" command to output the shape as a map (filled with 1s inside the shape, zeroes outside, maybe with an optional soft edge and an ongrid option)? This would be very convenient for making simple geometrical masks for cryoEM (e.g soft cylindrical masks for classification within a nanodisc). I currently do this using "shape cylinder", use the cylinder to mask the map, and then gaussian filter the resulting masked map to the point where I can choose a threshold that conforms to the shape, but having a way to do the same thing more directly would be very nice to have. Cheers Oli

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Sequential model display controls bound to buttonpanel button?
by Oliver Clarke 19 Jan '24

19 Jan '24

Hi all, I really like the new sequential model display controls in the daily build - thank you so much for implementing these! Would it be possible to add them as a command, e.g. nextmodel and prevmodel? This way I could add them to my box of buttons, and have them in the main GUI window, without needing to switch over to the model panel. Cheers Oli

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Re: Increase cofactor size
by Tristan Croll 19 Jan '24

19 Jan '24

(disclaimer: you should probably follow Elaine’s much more extensive advice) “atomspec” just refers to any selection string - e.g. “#1/A:50”, “:LIG”, “sel” etc. On Fri, 19 Jan 2024 at 18:52, Cameron Larson <cllarson(a)ucdavis.edu> wrote: > Thank you for your help. > A silly question, but what is might 'atomspec' be? a range of atoms? > > Thank you, Tristan > > On Fri, Jan 19, 2024 at 11:51 AM Tristan Croll <tcroll(a)altoslabs.com> > wrote: > >> Try "setattr {atomspec} bonds radius {value in Angstroms}". >> >> Best, >> Tristan >> >> On Fri, Jan 19, 2024 at 4:28 PM Cameron Larson via ChimeraX-users < >> chimerax-users(a)cgl.ucsf.edu> wrote: >> >>> Hello, >>> >>> I am using chimeraX to visualize a ligand. I am familiar with the >>> commands to increase protein thickness ('cartoon style protein thickness') >>> but how can I do this for a ligand or other molecule? >>> >>> Really appreciate the help, >>> >>> -Cameron Larson >>> _______________________________________________ >>> 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/ >>> >> >> Altos Labs UK Limited | England | Company reg 13484917 >> Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, >> United Kingdom, WA14 2DT >> <https://www.google.com/maps/search/1+Ashley+Road,+Altrincham,+Cheshire,+Uni…> >> > -- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT

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Increase cofactor size
by Cameron Larson 19 Jan '24

19 Jan '24

Hello, I am using chimeraX to visualize a ligand. I am familiar with the commands to increase protein thickness ('cartoon style protein thickness') but how can I do this for a ligand or other molecule? Really appreciate the help, -Cameron Larson

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