- ChimeraX-users - RBVI Mailing Lists

ChimeraX not communicating with GPU
by #TAN YONG JUN EDDIE# 20 Mar '25

20 Mar '25

Dear Developers, Hope this email finds you well. I have encounter an issue regarding the GPU driver usage for chimeraX. The issue is that the model and density movement is very choppy at step size 1, with a box size of 400. Here are some information on the software that I am using. Downloaded Software: Ubuntu 22.04 (Linux) ucsf-chimerax_1.9ubuntu22.04_amd64.deb<https://www.cgl.ucsf.edu/chimerax/cgi-bin/secure/chimerax-get.py?file=1.9/u…> This is my current nvidia driver and cuda version: NVIDIA-SMI 560.35.05 Driver Version: 560.35.05 CUDA Version: 12.6 It came to my attention that it is not utilising GPU upon running "graphics driver" on chimeraX, which outputs: graphics driver OpenGL version: 4.5 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.3 OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits) OpenGL vendor: Mesa additionally, it is not showing up under nvidia-smi when I am running the program. Is there any solutions to this issue? Thank you in advance. Regards, Eddie

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Protein-Protein Interaction Prediction
by Charity Conlin 19 Mar '25

19 Mar '25

Hello, I am trying to use ChimeraX to predict the interaction of 2 proteins using alphafold: Beta-Lactoglobulin and Lactoferrin. I have plugged the 2 protein sequences into the alphafold tool to try to predict the interaction, but I get a failure code in google colab. I am wondering how I can get around this? I think it is because the wrong versions of numpy and colab are installed during the program. Thanks, Charity [cid:b73a7660-3878-48cf-87d5-ddcd6ab388c2]

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Poor performance on Ubuntu w/ discrete graphics vs basic b laptop
by ben 19 Mar '25

19 Mar '25

I'm looking for trouble shooting tips on poor graphics performance on linux. I have read through the FAQ's and done a basic search of the chimera list. Observed: Symptom: Prohibitively slow rendering when just rotating a map, especially if a model is loaded as well. When using Isolde (and presumably anything with clipper) performance is more "normal" as only a small portion of the map is displayed. System: This is observed on Ubuntu distros (both 20.04 22.04) with their respective Chimerax packages, tested versions 1.6.1 and 1.9. Nvidia drivers installed via the cuda toolkit (535.183.01 CUDA Version: 12.2 ) GPUs are either rtx 3090 or 4090s Point of reference: Performance is compared to my relatively very underpowered Windows thinkpad w/o discreet graphics. Thanks for any pointers to resources! Ben Sent with [Proton Mail](https://proton.me/mail/home) secure email.

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Issue with crashing after mac upgrade to Sequoia
by Lee, Juliet A. 19 Mar '25

19 Mar '25

Hello! I recently updated my Mac (M2) to Sequoia 15.3.2, and I have had a specific issue in ChimeraX since then (though I cannot be 100% positive the two things are linked). Basically - whenever I try to save (anything) in ChimeraX, the application stops responding and I have to quit it. I downloaded the newest version 1.9 of ChimeraX as well as the daily build version - but this problem persists. I read about issues with the graphics driver - but these seem to be limited to Intel chips... Hoping you might have some insight as to why this is occurring, thank you!!! Sincerely, Juliet

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secondary structures
by Bajaj, Ruchika 18 Mar '25

18 Mar '25

Hi I want to determine helices and betasheet and their ranges in a structure. Could you please let me know which command and its usage I can use to get it. Please let me know. Thanks !! Regards Ruchika

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Request for Review of Figure 12 instructions
by Zeenat Bashir 18 Mar '25

18 Mar '25

Dear ChimeraX Developers, I hope this email finds you well! I am developing a hands-on module for students using ChimeraX, and I want to express my appreciation for this powerful and beautifully designed tool. I would like to request a review of the instructions on page 11 for generating Figure 12. I have successfully generated this figure before and am now attempting to do so using ChimeraX. However, I would appreciate your guidance to ensure the accuracy and clarity of the instructions (I have highlighted it in red) Thank you for your time and support! I look forward to your feedback. Best Regards, Zeenat -- *Dr. Zeenat Bashir* *Senior Lecturer* *Biotechnology Lab Coordinator* *Department of Chemical and Biomolecular Engineering* *University of Pennsylvania* *310 Towne Building* *220 S. 33rd Street* *Philadelphia, 19104 -6393* bashirz(a)seas.upenn.edu

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sybyl vs amber atom types in ChimeraX
by laurene.jacquot 17 Mar '25

17 Mar '25

Dear ChimeraX community, I hope this message finds you well. I am a master student currently working on a project where I need to generate a mol2 file with amber atom types for a protein. Chimera does not manage to parametrize my protein at all, which is why I switched to ChimeraX. ChimeraX does manage to generate a mol2 file, but it writes sybyl atom types. Despite looking on forums, I have not found a feature like in Chimera to write amber atom types instead. I was wondering if such a feature exists in ChimeraX ? Thanks in advance, Best, Laurène Jacquot PSL University, ChimieParisTech

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Automating the process of data generation via ChimeraX
by mishra.ananya.163＠gmail.com 17 Mar '25

17 Mar '25

Dear Sir/Madam, I am an undergraduate student working on a project and I am trying to generate values for the solvent accessible surface area, mean molecular lipophilicity potential and mean surface electrostatic potential for a dataset involving protein 3D structures (in pdb format). We also plan to introduce point mutations via ChimeraX using the swapaa command and measure the same values for the mutated proteins. As such, we were wondering if there is a way to automate this process of generating the values for each protein, without having to manually do it. We tried to test out some code to see if it is possible to run a python file in ChimeraX. This was the code we wrote: import chimerax import csv import os from chimerax.core.commands import run run(session, "open" + r'C:\Users\anany\Downloads\Research\Test_PDB_Passenger\P35579_MYH9.pdb') run(session, "color red") run("surf") However, we received this error message: openC:\Users\anany\Downloads\Research\Test_PDB_Passenger\P35579_MYH9.pdb Traceback (most recent call last): File "C:\Users\anany\Downloads\Research\Test_PDB_Passenger\test_import.py", line 6, in <module> run(session, "open" + r'C:\Users\anany\Downloads\Research\Test_PDB_Passenger\P35579_MYH9.pdb') File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3156, in run raise UserError(self._error) chimerax.core.errors.UserError: Unknown command: openC:\Users\anany\Downloads\Research\Test_PDB_Passenger\P35579_MYH9.pdb Error opening python file C:\Users\anany\Downloads\Research\Test_PDB_Passenger\test_import.py We would appreciate your kind assistance! Thank you!

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Feature request alphafold: return selection when dragging in PAE plot
by Vorländer,Matthias Kopano 17 Mar '25

17 Mar '25

Dear ChimeraX team, I love the alphafold tools in ChimeraX, and have a small suggestion to make it even better. Currently, when associating a PAE plot from a JSON file, you can drag the mouse in the PAE plot to color the corresponding residues (magenta and lime), but the residues do not become selected (although the color command gets printed in the log). I think it would be helpful if there was an option (or default behavior) to return a selection in addition, so that the selected region could be saved as a named selection, the display style changed ect… Or am I missing anything? Many thanks in advance, Matthias

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Fwd: Re: coloring surfaces by electrostatic potential from different atoms
by Boaz Shaanan 16 Mar '25

16 Mar '25

Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel ---------- Forwarded message ---------- From: Boaz Shaanan <bshaanan(a)bgu.ac.il> Date: Mar 16, 2025 18:32 Subject: Re: coloring surfaces by electrostatic potential from different atoms To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Cc: Hi Elaine, Thank you so much for the prompt an informative reply. The points about the offset and dielectric are very relevant. In fact, in a quick test that I ran before posing the question I noticed that the coloring of the electrostatic potential on the cofactor was quie dim, probably because of those parameters. I'll also look into the MOLE and pseudo atom coloring. Thanks again. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Mar 16, 2025 17:50, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: Hi Boaz, I changed the subject line to try to describe this topic. We aren't the APBS experts but my understanding is that yes, it will generate potential at all points in the rectangular grid, based on the input atoms charges and locations. There will of course be potential values even at grid points where there are no atoms, since electrostatics are fairly long-range interactions. However, the magnitude will depend on what dielectric parameters you have given the calculation. Whether it makes sense: that is somewhat up to your scientific judgement. In my opinion, yes, it makes sense, but you have to think carefully about the "offset" you use to color the cofactor surface. Normally when the surface is on the same atoms that produced the charge, you use a positive offset (default 1.4) to color by values projected that distance outward from the surface, to represent what other outside atoms might "see". If you are coloring a surface of the cofactor atoms to try to understand the potential from the protein that the cofactor "sees," you should consider instead using a negative (say -1.4) or zero offset. The offset is adjustable in the Surface Color dialog options and the "color electrostatic" command: <https://protect.checkpoint.com/v2/r02/___https://rbvi.ucsf.edu/chimerax/doc…> <https://protect.checkpoint.com/v2/r02/___https://rbvi.ucsf.edu/chimerax/doc…> Note that an analogous procedure could be done in ChimeraX with the Coulombic electrostatic potential. For example, see the MOLE channels tutorial where we calculate the Coulombic potential from the protein but then show a surface on pseudoatoms representing a channel calculated by MOLEonline, and then color that channel surface by the protein potential. <https://protect.checkpoint.com/v2/r02/___https://www.rbvi.ucsf.edu/chimerax…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 15, 2025, at 10:30 AM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi friends, > On a related issue: > I'd like to explore the effect of replacing Val by Asp on the electrostatic potential 'seen' by a cofactor which is completely surrounded by the protein (this is relevant for understanding the change in reaction rate following such replacement). I thought of the following steps: > > • Omit the cofactor from the pdb2pqr and APBS. > • Read into chimerax the complete pdb (i.e. including the cofactor). > • Generate the surfaces (protein and cofactor). > • Render the electrostatic potential on both surfaces (i.e. Cofactor and protein surrounding it) and probe the potential on the cofactor. > • Does it make sense? Does APBS generate potential values in the void where the cofactor resides even though it wasn't present in the input pdb2pqr (i.e. in the void where the cofactor resides). > I'd appreciate your input. > Boaz >

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Re: ChimeraX-users Digest, Vol 99, Issue 28
by Boaz Shaanan 16 Mar '25

16 Mar '25

Hi friends, On a related issue: I'd like to explore the effect of replacing Val by Asp on the electrostatic potential 'seen' by a cofactor which is completely surrounded by the protein (this is relevant for understanding the change in reaction rate following such replacement). I thought of the following steps: 1. Omit the cofactor from the pdb2pqr and APBS. 2. Read into chimerax the complete pdb (i.e. including the cofactor). 3. Generate the surfaces (protein and cofactor). 4. Render the electrostatic potential on both surfaces (i.e. Cofactor and protein surrounding it) and probe the potential on the cofactor. 5. Does it make sense? Does APBS generate potential values in the void where the cofactor resides even though it wasn't present in the input pdb2pqr (i.e. in the void where the cofactor resides). I'd appreciate your input. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il ________________________________ From: chimerax-users-request(a)cgl.ucsf.edu <chimerax-users-request(a)cgl.ucsf.edu> Sent: Friday, 14 March 2025 21:00 To: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> Subject: ChimeraX-users Digest, Vol 99, Issue 28 Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..." Today's Topics: 1. sybyl vs amber atom types in ChimeraX (laurene.jacquot) 2. Re: sybyl vs amber atom types in ChimeraX (David A Case) ---------------------------------------------------------------------- Message: 1 Date: Fri, 14 Mar 2025 09:47:39 +0000 From: "laurene.jacquot" <laurene.jacquot(a)etu.chimieparistech.psl.eu> Subject: [chimerax-users] sybyl vs amber atom types in ChimeraX To: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> Message-ID: <MR1P264MB2612AFE1D7D6BEF80D0B069A92D22(a)MR1P264MB2612.FRA P264.PROD.OUTLOOK.COM> Content-Type: multipart/alternative; boundary="_000_MR1P264MB2612AF E1D7D6BEF80D0B069A92D22MR1P264MB2612FRAP_" Dear ChimeraX community, I hope this message finds you well. I am a master student currently working on a project where I need to generate a mol2 file with amber atom types for a protein. Chimera does not manage to parametrize my protein at all, which is why I switched to ChimeraX. ChimeraX does manage to generate a mol2 file, but it writes sybyl atom types. Despite looking on forums, I have not found a feature like in Chimera to write amber atom types instead. I was wondering if such a feature exists in ChimeraX ? Thanks in advance, Best, Laurène Jacquot PSL University, ChimieParisTech -------------- next part -------------- A message part incompatible with plain text digests has been removed ... Name: not available Type: text/html Size: 3823 bytes Desc: not available ------------------------------ Message: 2 Date: Fri, 14 Mar 2025 09:08:36 -0600 From: David A Case <dacase1(a)gmail.com> Subject: [chimerax-users] Re: sybyl vs amber atom types in ChimeraX To: "laurene.jacquot" <laurene.jacquot(a)etu.chimieparistech.psl.eu>, chimerax-users(a)cgl.ucsf.edu Message-ID: <20250314150836.x2iskz4ufcygpsqt(a)pop-os.localdomain> Content-Type: text/plain; charset=us-ascii; format=flowed On Fri, Mar 14, 2025, laurene.jacquot via ChimeraX-users wrote: > >I am a master student currently working on a project where I need to >generate a mol2 file with amber atom types for a protein. I don't have a ChimeraX answer here, but rather a question: why do you need a protein mol2 file with Amber atom types? Amber workflows would not create a mol2 file for an entire protein; but of course, you may need such a file for some other purpose. If so, we may be able to find some Amber tools that does this (or avoids needing it), if the ChimeraX folks themselves don't have a solution. ....dave case ------------------------------ Subject: Digest Footer _______________________________________________ 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://protect.checkpoint.com/v2/r02/___https://mail.cgl.ucsf.edu/mailman/… ------------------------------ End of ChimeraX-users Digest, Vol 99, Issue 28 **********************************************

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Ubuntu 24 ARM Daily Builds
by Zach Pearson 15 Mar '25

15 Mar '25

ARM daily builds for Ubuntu 24.04 are now available. — Zach

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Feature suggestion: cubic interpolation for image display
by Ricardo Righetto 14 Mar '25

14 Mar '25

Dear ChimeraX team, (I have a vague memory of discussing this before, apologies if duplicate!) When displaying volumes as images (e.g. cryo-ET volume slices), I see that by default it uses linear interpolation: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#style Would it be possible to offer higher-order interpolation options such as cubic? I love how customizable it is to make figures in ChimeraX, but this is the one feature that we really miss compared e.g. to 3dmod from IMOD. Thank you! -- Ricardo Diogo Righetto

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Dockprep Inquiry
by Emir MALOVIC 13 Mar '25

13 Mar '25

Hello, I am trying to perform some simple docking between a small molecule and a protein. I get the following warning: (UNL) `bash.exe: warning: could not find /tmp, please create!` I was browsing around and noticed I may need to set up ChimeraX Development Environment. Is this true? Thank you, Emir

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ISOLDE refine.eff and phenix.refine
by Shawn Rumrill 13 Mar '25

13 Mar '25

Dear ChimeraX Community, Not strictly ChimeraX related, but probably interesting to some and I've seen some feedback for ISOLDE here... I am using ISOLDE to rebuild a mid-resolution protein/NA model (still adjusting to using ISOLDE, but really powerful tool). I want to refine using phenix.refine, but I am running into a problem with the refine.eff file. The error from the terminal output is below. I've gathered that this is due to a change in parameter terminology from Phenix 1.20 to 1.21. My question is, is there some way to write the refine.eff file with the required information? I would hate to have to manually edit the .eff output file each time I want to run a new refinement in Phenix. Thanks, Shawn Error: Processing files: ------------------------------------------------------------------------------- Found phil, refine.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ refine.eff Unrecognized PHIL parameters: ----------------------------- refinement.input.pdb.file_name (file "refine.eff", line 6) refinement.input.xray_data.file_name (file "refine.eff", line 9) refinement.input.xray_data.labels (file "refine.eff", line 10) refinement.input.xray_data.high_resolution (file "refine.eff", line 11) refinement.input.xray_data.low_resolution (file "refine.eff", line 12) refinement.input.xray_data.r_free_flags.file_name (file "refine.eff", line 14) refinement.input.xray_data.r_free_flags.label (file "refine.eff", line 15) refinement.input.xray_data.r_free_flags.test_flag_value (file "refine.eff", line 16) Sorry: Some PHIL parameters are not recognized by phenix.refine. Please run this program with the --show-defaults option to see what parameters are available. PHIL parameters in files should be fully specified (e.g. "output.overwrite" instead of just "overwrite")

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Re: Inquiry to docking protein onto lipid bilayer
by You, Youngki 12 Mar '25

12 Mar '25

Hello Tommy, You can use this server (PPM in OPM site), https://opm.phar.umich.edu/ppm_server3_cgopm , to determine the orientation and depth of your protein in the membranes. After that, you can use the model from PPM in CHARMM-GUI. Best, Youngki ________________________________PNNL__ Youngki You, PhD Post Doctorate RA, Biochemical Mechanisms Structure, Function & Design Biological Sciences Division Pacific Northwest National Laboratory Tel: +1 (509) 371-6660

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Inquiry to docking protein onto lipid bilayer
by Tommy Tong 12 Mar '25

12 Mar '25

Dear ChimeraX experts, Good afternoon. My name is Tommy from San Diego Biomed. I am a beginner to ChimeraX version 1.9. May I ask if it is possible to use ChimeraX to dock a membrane protein into a lipid bilayer? I obtained Phosphotidylcholine bilayer (POPC) structure from CHARMM-GUI webpage https://charmm-gui.org/?doc=archive&lib=lipid_pure, and was wondering if it is possible to “place” a protein into this POPC structure in ChimeraX. Your help and advice on this is greatly appreciated. Thank you. Sincerely, Tommy

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Obtain individual RMSD values
by javisanchezdelrio＠gmail.com 12 Mar '25

12 Mar '25

Hello, I have an issue when applying matchmaker command in ChimeraX. When I execute the command: matchmaker #1 to #2 showAlignment true I obtain the alignment with the bars in the upper layer showing the individual RMSD of each residue. But the results yields the overall RMSD of the alignment (i.e. RMSD between 108 pruned atoms). Is there any way to obtain those individual RMSDs of the alignment as a file or have them printed in the log for post-processing? Thank you in advance

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Dividing a huge model (& map) into smaller chunks
by Alejandro Buschiazzo 12 Mar '25

12 Mar '25

Dear chimeraX developers/users Using version 1.9, I am trying to divide a very big mmcif model (230K + nonH atoms; >130 chains) and corresponding mrc map, into a number of smaller mmcif files (and corresponding cropped maps, covering just those parts). What I’ve tried so far unsuccessfully: I can create dummy atoms with build start atom, at desired x,y,z points, so that I can then use select zone to select a radius and keep parts near each dummy atom. Yet, that is suboptimal: I would largely prefer to keep (build) boxes, and not spheres, ensuring complete recovery and no blind spots. So that each box slightly overlaps with the neighboring one, and systematically covers the whole original map volume. 1. How can I generate a script that will do this "systematic windowing” screening, making boxes of a defined side-length at each step, and keeping the model within? 2. How should I then crop the original map, so that it covers each box (with a small padding on the borders)? 3. How should I stitch back the models, so that I don’t loose any atomic coordinates information? (of course that stitching will be done after I do some refinement work on each boxed model vs map) So sorry for the many questions! I’ve been trying hard to find this kind of strategy, and just can’t seem to succeed…. Thank you very much in advance Alejandro -- Alejandro Buschiazzo, PhD Associate Professor Laboratory of Molecular & Structural Microbiology Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 ext. 120 Fax: +598 25224185 https://pasteur.uy/en/laboratories/molecular-and-structural-microbiology/

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General ?s - Foldseek (Sequence Plot) and Similar Structures Table
by Emir MALOVIC 11 Mar '25

11 Mar '25

Hello, Quick question: When I load the sequence plot, I receive 2 sequence images separated by a very large black space. When I save the image as a PNG, the black space between the sequence images is retained. Basically, the image is mostly black space. Is there a way to change that or is this a bug? Am I able to somehow copy the Similar Structures table or export it into Excel? A copy/paste function would be ideal and quick. I am using the Chimera 1.10 dev. Please let me know at your earliest convenience! Thank you, Emir

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Suggestion for improvement
by James Raymond 11 Mar '25

11 Mar '25

I love ChimeraX and use it often for my work, e.g. this one <https://www.pnas.org/doi/10.1073/pnas.2421910122>. When using AlphaFold to predict protein structure, the sequence is pasted into the sequence box. It does not allow entering the fasta name ">name" before the sequence.. Allowing a name to be included can avoid much confusion. Presently, the screen shows the output as "best_model" which becomes very confusing when several best models are shown on the screen. James Raymond Univ. Nevada Las Vegas

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What is the .exe file for ChimeraX Toolbox?
by m.i.bashir＠bham.ac.uk 11 Mar '25

11 Mar '25

Hi all, First time posting here. I'm looking to find the name and location of the file/folder that manages the ChimeraX in-app browser. The way I launch the browser is to go to 'tools' in the top bar, then press 'more tools', and then it brings up the ChimeraX Toolshed Where is the .exe file that controls this in app browser? I am attempting to find the .exe file and black list it, so we can use ChimeraX for an exam Thanks,

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SASA in MDS
by Gabriel López Velázquez 10 Mar '25

10 Mar '25

Dear Elaine, I am sorry; I did not state the subject of my previous email. I would ask for help. How can I calculate SASA as a function of time from the MD simulations in Chimerax? What archives need to perform it? Thanks in advance! Gabriel.

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(no subject)
by Gabriel López Velázquez 10 Mar '25

10 Mar '25

Dear Elaine, I would ask for help. How can I calculate SASA as a function of time from the MD simulations in Chimerax? What archives need to perform it? Thanks in advance! Gabriel.

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Inquiry About Favorable Contacts and Display Methods in ChimeraX
by 田畑　健士郎 07 Mar '25

07 Mar '25

Subject: Inquiry About Favorable Contacts and Display Methods in ChimeraX Dear ChimeraX Developers, My name is Kenshiro Tabata. I hope this email finds you well. I am currently using ChimeraX to analyze the effects of point mutations on protein structure, particularly in cases where a larger side chain (e.g., methionine) is replaced by a smaller one (e.g., valine). In such cases, I expect that interactions with the opposing amino acids may be reduced due to the decreased side-chain volume. To investigate this, I would like to ask for your guidance regarding the interpretation and visualization of favorable contacts. ________________________________ 1) Understanding Favorable Contacts I understand that the contacts command identifies all types of interactions, whereas the clashes command detects only unfavorable interactions. Based on this, I interpreted the positive VDW overlap as indicating unfavorable (repulsive) interactions, while an overlap between 0 and -0.4 represents favorable (attractive) interactions. Could you confirm if this understanding is correct? ________________________________ 2) Best Approach for Displaying Only Favorable Contacts To analyze how the mutation affects interactions, I would like to display only favorable contacts. Below is the approach I have considered: Proposed Approach 1. Retrieve all interactions (favorable, neutral, and unfavorable) using the contacts command contacts overlapCutoff -0.4 saveFile all_contacts.txt 2. Retrieve only neutral and unfavorable interactions contacts overlapCutoff 0 saveFile non_favorable_contacts.txt 3. Compute the difference between these two sets using Python, extract only favorable contacts, and format them into a ChimeraX pseudobond file # File paths all_contacts_path = "all_contacts.txt" non_favorable_contacts_path = "non_favorable_contacts.txt" favorable_contacts_path = "favorable_contacts.pb" # Read files with open(all_contacts_path, "r") as f: all_contacts = set(f.readlines()) with open(non_favorable_contacts_path, "r") as f: non_favorable_contacts = set(f.readlines()) # Extract favorable contacts favorable_contacts = all_contacts - non_favorable_contacts # Convert to ChimeraX pseudobond file format with open(favorable_contacts_path, "w") as f: f.write("; Pseudobond file for favorable contacts\n") f.write("; radius = 0.1\n; color = green\n; dashes = 6\n") for line in favorable_contacts: parts = line.strip().split() if len(parts) >= 4: atom1 = f"/{parts[0]}:{parts[1]}@{parts[2]}" atom2 = f"/{parts[3]}:{parts[4]}@{parts[5]}" f.write(f"{atom1} {atom2}\n") 4. Load the extracted favorable contacts into ChimeraX for visualization open favorable_contacts.pb Would this be an appropriate approach? Alternatively, is there a simpler or more precise way to achieve this in ChimeraX? I appreciate your time and assistance, and I look forward to your advice. Best regards, Kenshiro Tabata

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AI in ChimeraX
by Elaine Meng 07 Mar '25

07 Mar '25

On Mar 7, 2025, at 6:01 AM, Veach, Kevin G. <kevin.veach(a)uky.edu> wrote: > > Hi Elaine: > Does Chimera-X use Artificial Intelligence or Large Language Learning Models? > Thank you, > > Kevin > Kevin Veach, Computer Support Specialist II > University of Kentucky, Animal & Food Sciences Dept. Hi Kevin, Please use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address CC'd here for general questions about ChimeraX -- I'm not the top expert on all parts of ChimeraX, so you may get better answers from other developers or our user community. Regarding your question, my understanding is that ChimeraX itself does not use these kinds of calculations, but it has tools that interface to web services or other calculations (run outside of ChimeraX) that do use them. The ones that I can think of are AlphaFold/ColabFold and ESMFold: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html#predict> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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Creating movie in ChimeraX from YASARA simulation
by ibogdanov 07 Mar '25

07 Mar '25

Hi ! I have the following question - How can I create a movie, when I cannot use the YASARA.sce file from which I converted/extracted xtc.file(the trajectories) when I have all the snapshots(pdb and sim.files) created as separate files during the performed simulation in YASARA...I've uploaded for example the first pdb file of the series and the xtc.file but isn't the saved xtc.file(trajectories) of the whole simulation(for all the structures)? How would you suggest me to solve this problem, if ChimeraX doesn't support sce.files ? Thank you in advance! Kind Regards, Ivan Bogdanov

2 2

Problem installing on OSX
by Thom Hughes 06 Mar '25

06 Mar '25

I apologize for the dumb question, but here it is. I want to install the isolde extension. When I go to more tools, isolde, and click the install button a .whl file downloads correctly. But then nothing happens. I’m running OSX 15.3.1. thanks in advance for any pointers!

2 4

Unable to open the file after downloading ChimeraX
by Guo-Ping Zhou 05 Mar '25

05 Mar '25

Dear Sir/Madam, After downloading ChimeraX, I automatically get the attached .png in the application as a microsoft word file. However, I can't open the Quick Access Toolbar. Could you please tell me how to make it work? Thanks! Guo-Ping Zhou, Rocky Mount Life Sciences Institute, Rocky Mount, NC 27804

2 1

(no subject)
by FRANGIE Christian 05 Mar '25

05 Mar '25

Dear UCSF ChimeraX Support Team, My name is Christian frangieh, I am currently using Chimera X to visualize my AlphaFold simulations, and I want to check when i introduce a mutation and change one residue (amino acid), whether there is a change in the surface accessibility of the residue. Currenlty i am checking this visually by checking whether the residue is exposed to the surface or hidden. Nevertheless, i would like to know how can i do this with a command or by some form of calculation or structural analysis. Can you please help me with this matter? Warm Regards, Christian

2 2

Can not find Structure Minimization in ChimeraX menu
by N.B. Nugroho 04 Mar '25

04 Mar '25

Dear ChimeraX developers I a little bit confuse to find the Structure Minimization menu in ChimeraX. In Chimera 1.16 it located in menu Tools>Structure Editing>Minimize Structure. Could you please guide me for this little problem. Best regards Nuki B Nugroho

2 1

(no subject)
by junjie han 02 Mar '25

02 Mar '25

Hi, I hope you are doing well. May I ask two questions? First one: Why does the connection part between the side chain and backbone, which is circled in a dashed line in ChimeraX, look so abnormal? How can I make it display normally? [cid:437c0c59-2e31-4251-ac9c-eff3f64af0dd] Second one: Is it possible to show the border only for a specific region of protein without hiding other regions? Thanks, Junjie

2 1

define integer attributes for multiple individual pseudobonds
by hannes.ludewig＠googlemail.com 28 Feb '25

28 Feb '25

Dear developers, I am trying to color pseudobonds by an individual (per-bond) attribute value (integer). I seem to be unable to use .pb files to create individual pseudobonds. And when I am using the pbond command several times providing an individual name for each pseudobond thus creating individual models (#1.1, #1.2, etc) I am unable to assign an attribute and color all pseudobonds according to the corresponding attribute value. What I want to create is similar to the alphafold contacts colored by PAE. Only that the values I am providing aren't PAE and I would like to determine the residue pairs that form each pseudobond. I apologize in case I am overlooking something obvious, but your help and/or clarification would be very much appreciated. Thank you. Best wishes, Hannes

3 2

Disulphide bridges in ISOLDE
by Guillaume Gaullier 28 Feb '25

28 Feb '25

Hello ISOLDE users and Tristan, Is there a distance threshold at which ISOLDE won't let me close a disulphide bridge? I am puzzled, because it seems I can close a disulphide between two Cys about 10 residues apart in sequence and quite far from each other in space. In fact much further apart than a bond length, so the resulting bond looks ridiculously stretched. But it is quickly fixed when running a local simulation, even if it needs to pull the backbone out of density to achieve a reasonable S-S bond length. In the same model, I have two other Cys that follow each other in sequence. When loading the AlphaFold prediction, the two S atoms are close enough (for some reason) that ISOLDE offers to make the disulphide, so I say yes. Later on, wanting to test both options to assess which one is best supported by the map, I can break this disulphide, but once I do there is no way to close it again. In this case, the two S atoms settle about 3.4 Å apart when removing the bond, which is longer than an ideal disulphide, but much shorter than the distance over which ISOLDE still allowed me to form a disulphide in the first case. The documentation doesn't say anything about disulphides (or somehow I missed it). In fact, there seems to be no command to operate on disulphides? Using the menu item does not write anything to the Log, so if there is a command I cannot find what it is and what options it might accept. If someone can help with this, I would appreciate it! Thank you, Guillaume --- Guillaume Gaullier, PhD Researcher, Blikstad group Molecular Biomimetics / Microbial Chemistry Department of Chemistry - Ångström Uppsala University Lägerhyddsvägen 1 752 37 Uppsala Sweden 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

3 6

Assistance Required: Extracting List of Interacting Residues within 4 Å in UCSF Chimera
by Rashmi Aggarwal 27 Feb '25

27 Feb '25

Dear UCSF Chimera Support Team, I hope this message finds you well. I am currently working on analyzing interactions between two molecular structures using UCSF Chimera. I have successfully identified residues that are within a 4 Å distance between the two molecules. However, I am encountering difficulties in obtaining a clear, textual list of these interacting residues, as reading them directly from the visual representation is challenging. Could you please provide guidance on the specific commands or procedures within Chimera that would allow me to: 1. *Select residues* in one molecule that are within 4 Å of the other molecule. 2. *Generate and export a list* of these selected residues for further analysis. I have attempted various selection and reporting commands but have not yet achieved the desired outcome. Detailed instructions or references to relevant documentation would be greatly appreciated. Thank you very much for your assistance. Best regards, Rashmi

2 2

Show side chain, main chain, and cartoon at the same time
by Zhang, Miao 27 Feb '25

27 Feb '25

Dear colleagues I am new to ChimeraX. I am trying to figure out how to show side chain, main chain, and cartoon at the same time in a protein structure. Like the one below made in other software. Could you please help? [cid:image001.png@01D9D154.CE3D4440] Best, - - - - - - - - - - - - - - - - - Miao Zhang Ph.D. Associate Professor Chapman University School of Pharmacy 9401 Jeronimo Rd, Suite 297W Irvine, CA 92618 Phone: 714-516-5478 http://www.chapman.edu/our-faculty/miao-zhang

2 24

Cannot click popup windows in ChimeraX WSL installation
by Jobichen 26 Feb '25

26 Feb '25

Hi All,I am unable to click on any popup windows in my chimeraX installation. For eg: colour menu, once popped up, unable to click on any options.Ubuntu 22.04.5 LTS installed under WSL in Dell laptop. ChimeraX ver 1.9Error messages:NOTE: available bundle cache has not been initialized yetmalloc(): unsorted double linked list corruptedAborted (core dumped) Any suggestions.Thank you.Jobi

4 8

Rotation using left mouse button
by y.v.hazendonk＠nki.nl 26 Feb '25

26 Feb '25

Hello, In my work with ChimeraX I have to rotate my proteins quite a lot to get a good look at different residues and helices. My problem is that very often when I am rotating my protein using the left mouse button, another piece of my protein will glide across my screen in the foreground, at which point the axis of rotation will lock onto this other piece. Is there a way to disable this unwanted locking? I am fine with these pieces floating across the foreground, as long as my axis of rotation doesn't suddenly lock onto them. I want the rotational axis to stay where it was when I started rotating. I look forward to your reply on how to fix this issue. Thank you in advance. With kind regards, Yorick van Hazendonk

5 6

Communicate between multiple ChimeraX instances
by Roden Deng Luo 25 Feb '25

25 Feb '25

Hi, I wonder if there is a way to synchronize two or more ChimeraX instances/sessions. For example, sync the camera. The meeting command ( https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/meeting.html) a great command I just got to know, is very close to what I am looking for. Only I will have different data in different instances, and toggles to enable and disable what features to be synced. If it is not currently implemented, how should I approach it as a developer? Many thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

3 3

Measure angle between domains in chimeraX
by junjie han 24 Feb '25

24 Feb '25

Hi Elaine, I hope this email finds you well. May I ask how to measure the angle between two domains from one molecule or two different molecules in ChimeraX. Here are some examples below. Example 1: [cid:ee5ac0af-a9be-4e98-bb7c-e555c8f183c2] How to calculate these angles (54°, 38°)？ Example 2: [cid:24512415-5303-4be2-8f61-a4fd6acdc0ee] How to calculate this angle (75°) ? Example 3: [cid:f3ed355d-a961-4647-8a3c-b39ab3875cb8] How can I measure the rotation angle between A and B, or between two specific regions of these two molecules in ChimeraX? If I need to calculate the rotation angles of two molecules relative to a specific molecule, how can I define a shared axis for calculating the rotation angles? The rotation axes are different when I use the command “measure rotation A toModel B” to calculate the rotation angles, which is not an ideal way to compare them in parallel. Thank you in advance for your any suggestions. Very appreciated, Junjie

3 16

Trouble Morphing 2 Proteins
by Andrew Mejia Garnica 24 Feb '25

24 Feb '25

Hello, I have been using ChimeraX with a mac book from 2020 with a 1.1 GHz Dual-Core Intel Core i3, Intel Iris Plus Graphics 1536 MB and 8 GB of RAM. Everything seems to be working fine until I try to do a morph. Both proteins have been super positioned by matchmaker. I can only complete 5 frames out of the 60 with the command, morph #1,2 wrap true frames 60. However, I am not able to look through the frames, record or press play. I have tried it with the tutorial proteins as well and got stuck. The proteins that I am trying to morph will be attached to this email. I would like to ask if you could do a morphing for me or redirect me to be able to. I would also like to ask if it is a Graphis problem as I was also unsuccess full using a Dell laptop with a , 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHZ, 16GB of RAM, 64-bit operating system, x64-based processor. Thank you for your time and I hope to hear from you soon. Best, Andrew

2 5

Surface dust command in the .cxc script
by 李泽 24 Feb '25

24 Feb '25

Hi all: I'm trying to use the .cxc script to run the software, I found that the "surface dust" command has never been executed in it. Have anyone met the same problem? Any suggestions. Thank you all. Best, Ze

3 3

Freelance vs. Agency – Best Choice for Native App Developers Houston?
by hooria.khan＠algoace.com 23 Feb '25

23 Feb '25

I’m trying to decide whether I should hire a freelance developer or work with an agency for my native app development needs. Freelancers can be more affordable, but agencies offer structured project management. Are there any experienced <a href="https://algoace.com/houston-app-development/">Native App Developers Houston</a> who work independently and provide top-notch services? On the other hand, if you’ve worked with an agency, was the cost worth it? Any recommendations based on your experience?

1 0

Update chain description from fasta file
by Paul Sauer 23 Feb '25

23 Feb '25

Hi, I really like the 'sequence update' feature that was introduced in Chimerax 1.9. I was wondering if it is possible to expand the capability of this command to update the sequence description/ sequence name from the header line of an opened alignment or fasta file and write it out with the cif file. It seems like currently the full sequence is updated from an associated fasta file but the sequence names are being ignored. Could the sequence name written into the ' entity.pdbx_description' column in the resulting cif file? Or maybe there is already an option that I missed? Also, as a secondary feature request, maybe the sequence update command could not only write the ' entity_poly.pabx_seq_one_letter_code_can' table but also use the available coordinates and residue names of the structure to write the '_entity_ poly.pdbx_seq,_one_letter_ code' table for each polymer that includes modified residues/ligands etc in parentheses in addition to the canonical one letter code where known. I could imagine that these capabilities would make depositing coordinates of macromolecular complexes with many chains to the PDB much easier and more interactive, so maybe this would be helpful for other people as well. Thank you to the Chimerax team & contributors for creating such a great program, Paul

2 2

Dear ChimeraX users!
by amiraziznezhad＠gmail.com 23 Feb '25

23 Feb '25

Dear ChimeraX users! I am dealing with the analysis of protein-ligand interactions in a single PDB structure. I am looking for any tools implemented in Chimera-X, which could be used to analyse the interactions (besides the hbond and contact tools giving info in the log files msuic). I wonder to know which commands and corresponded ChimeraX tools could be used to produce the 2D contact diagrams shown on the Fig.4 as well as python graphs demonstrated on the Fig.5 in the Chimera-X article: https://www.myeasymusic.ir/ Many thanks in advance! Cheers Enrico

2 1

RspProp
by Robert Stanley 23 Feb '25

23 Feb '25

Hello - I was wondering what I have to do to install the RspProp tool? It doesn't appear in my utilities menu or the structure analysis one. I have version 1.9 (2024-12-11). I very much appreciate this program and use it in my Biochem and Biophysical Chemistry courses to expose the students to it ASAP. Thanks, Bob Stanley Robert J. Stanley, Ph.D. Professor of Chemistry 1901 N. 13th St., 250B Beury Hall Temple University Philadelphia, PA 19122 (215) 204-2027 https://www.cst.temple.edu/~rstanley/

3 2

Contribute to ChiemraX Recipe
by NG, Cheukhei Jackie [Student] 22 Feb '25

22 Feb '25

Dear ChimeraX Development Team, I am Jackie NG from a cryoEM group in the Hong Kong Polytechnic University interested in molecular visualization and analysis. I am writing to express my interest in contributing scripts to the ChimeraX library, specifically for inclusion in the ChimeraX Recipes. Sharing my scripts could benefit the community and enhance the utility of ChimeraX for various applications. The scripts are mainly quality-of-life improvements on copying selected parts of models, producing map-quality representations, organizing ligand chains, and many more. Please let me know if there is a process for submitting these scripts and any specific guidelines I should follow. I am eager to collaborate and contribute to the ongoing development of ChimeraX. Thank you for considering my contribution. I look forward to your response. Best regards, Jackie [https://www.polyu.edu.hk/emaildisclaimer/PolyU_Email_Signature-v2.jpg] Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.

2 2

Aligning fasta sequence with the sequence of pdb model in chimeraX
by Rayees Mattoo 21 Feb '25

21 Feb '25

Hi, I was wondering if there is a way in chimeraX to align fasta sequence with sequence from the loaded pdb model. Just wanted to be sure that the residue numbering matches the original Uniprot sequence. Any other suggestions that can do the job quickly are welcome. Best, Rayees

2 2

(no subject)
by FRANGIE Christian 21 Feb '25

21 Feb '25

Dear UCSF ChimeraX Support Team, My name is christian frangieh, I am currently using chimera x and i want to check the interacting residues that form the interface between 1 chain with 2 other different chains. for example my model has 3 chains (chain A,B,C) i want to have a list of the resideus of chain A and B that are interacting with chain C Can you please help me with this? Thank You

2 4

save clipped volume
by Yanhe Zhao 20 Feb '25

20 Feb '25

Greeting there ChimeraX developer and community, I have "clip" used on my map and currently want to save the clipped one as a new mrc file, what is the best way to do this? I checked the "save Map" command and found the region option, but I don't think it is the right option if I have my clip plan tilt. Thanks a lot for any input. Thanks and cheers, Yanhe

2 2

Help Needed with Building Capsid for ssRNA Homolog
by Bruno Hay Mele 20 Feb '25

20 Feb '25

Hi everyone, I am trying to build the capsid for a homolog of Chaetoceros socialis forma radians RNA virus 1 (PDB: 8b38). My approach was to work by homology, transferring the assembly/symmetry information from the PDB entry to my model, which I built by assembling homologs of the three subunits of 8b38. Unfortunately, this has not been as straightforward as I hoped. Ibm a complete newbie in this area, and my attempts to copy the relevant parts of the assembly information or use the ChimeraX bsymb tool have led nowhere. Could someone please point me to the right solution? Ibd really appreciate both: A practical solution: How to correctly transfer the symmetry information and generate the full capsid assembly in ChimeraX. Some references or explanations: Resources that explain why the solution works this way, so I can understand the underlying principles. Any help or pointers would be very much appreciated. Thank you very much for your time and assistance. Cheers, -- Bruno Hay Mele, PhD 2D-20, Biology Dept., University of Naples Federico II https://github.com/bhym/ | +39 081 67 9118

2 2

ChimeraX Model Joining
by Nieder, Claire 20 Feb '25

20 Feb '25

Hey there, I am a grad student at UConn trying to covalently link two PDB models by inserting a GFP into the third intracellular loop of 5HT4. If you have any advice, I would really appreciate it. Thanks, Claire Nieder Kienzler Lab UConn Chemistry

2 3

(no subject)
by FRANGIE Christian 20 Feb '25

20 Feb '25

Dear UCSF ChimeraX Support Team, My name is christian frangieh, I am currently using chimera x and i want to check the interacting residues that form the interface between 1 chain with 2 other different chains. for example my model has 3 chains (chain A,B,C) i want to have a list of the resideus of chain A and B that are interacting with chain C Can you please help me with this? Thank You christian

1 0

Re: [Chimera-users] script for clashes
by Eric Pettersen 18 Feb '25

18 Feb '25

Hi Valerio, Well, one of the main motivations for using ChimeraX is that running commands actually return results instead of nothing. So the 'clashes' command returns a dictionary of the clashes, as described here: https://github.com/RBVI/ChimeraX/blob/1bae62d955f4b9d6d05a31541af0372f11d36… . Therefore you do not need all that extra code that Chimera needs to try to determine if there were any clashes. Instead it's just: clashes = run(session, "clashes") if clashes: # code for existing clashes else: # code for no clashes Now, reasonable structures should have at most a few clashes, and usually zero, not many thousands like your structures seem to have. I suggest opening one of the structures interactively in ChimeraX, run the "clashes" commands and look to see why there so many clashes. --Eric > On Feb 17, 2025, at 3:03 AM, chiarini(a)takisbiotech.it wrote: > > Dear Prof Pettersen, > > Thank you so much for your advice. So far I managed to operate in chimeraX and now I can see the outputs of my script. righ now I'm running the following: > > > # -*- coding: utf-8 -*- > > import os > from chimerax.core.commands import run > > # Funzione principale che accetta la sessione > def process_pdb_files(session): > # Specifica la cartella con i file PDB > folder_path = "C:/Users/utente/Desktop" # Modifica il percorso della cartella > > # Stringa da cercare nei file > search_string = "A3a" > > # Lista dei file PDB nella cartella > file_names = [fn for fn in os.listdir(folder_path) if fn.endswith(".pdb")] > > # Stampa dei file trovati nella cartella per debugging > print("File trovati nella cartella:", file_names) > > # Loop su ogni file che contiene 'search_string' nel nome > for pdb_file in file_names: > if search_string in pdb_file: > pdb_path = os.path.join(folder_path, pdb_file) > > # Apre il file PDB > print(f"Apertura del file {pdb_file}...") > run(session, f"open {pdb_path}") > > # Calcola i clash (comando corretto per ChimeraX) > run(session, "clashes") > > # Verifica se ci sono clash > clashes_found = False > for m in session.models: > if getattr(m, 'category', None) == "contacts": > clashes_found = len(m.pseudoBonds) > 0 > if clashes_found: > break > > # Se ci sono clash, elimina il file > if clashes_found: > os.remove(pdb_path) > print(f"Clash trovati, il file {pdb_file} è stato eliminato.") > else: > print(f"Nessun clash trovato per {pdb_file}.") > > # Chiude il modello dopo averlo processato > run(session, "close all") > > # Questa parte assicura che la funzione venga chiamata correttamente > def main(session): > process_pdb_files(session) > > # Quando esegui lo script in ChimeraX, la sessione viene passata automaticamente > main(session) > > AND I GOT THE FOLLOWING OUTPUT: > > runscript C:/Users/utente/Desktop/chimera_script2.pyFile trovati nella cartella: ['A3a_structure_1.pdb', 'A3a_structure_2.pdb', 'A3a_structure_3.pdb', 'A3a_structure_4.pdb', 'A3a_structure_5.pdb'] > Apertura del file A3a_structure_1.pdb... > open C:/Users/utente/Desktop\A3a_structure_1.pdb > Chain information for A3a_structure_1.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes84336 clashes > Nessun clash trovato per A3a_structure_1.pdb. > close allApertura del file A3a_structure_2.pdb... > open C:/Users/utente/Desktop\A3a_structure_2.pdb > Chain information for A3a_structure_2.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes655434 clashes > Nessun clash trovato per A3a_structure_2.pdb. > close allApertura del file A3a_structure_3.pdb... > open C:/Users/utente/Desktop\A3a_structure_3.pdb > Chain information for A3a_structure_3.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes626886 clashes > Nessun clash trovato per A3a_structure_3.pdb. > close allApertura del file A3a_structure_4.pdb... > open C:/Users/utente/Desktop\A3a_structure_4.pdb > Chain information for A3a_structure_4.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes482406 clashes > Nessun clash trovato per A3a_structure_4.pdb. > close allApertura del file A3a_structure_5.pdb... > open C:/Users/utente/Desktop\A3a_structure_5.pdb > Chain information for A3a_structure_5.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes315894 clashes > Nessun clash trovato per A3a_structure_5.pdb. > close all > > > WHAT ELUDES ME IS THAT FOR EACH STRUCTURE CHIMERA FINDS LOT OF CLASHES BUT THEN RETURNS THE STATMENT "NO CLASH FOUND FOR STRUCTURE X". Why is that? I know these structures have lots of overlapping atoms and it also seems that chimera counts the class "clashes". But maybe it also includes contacts? > I would like to count only steric clashes and atoms superposition which makes the structure impossible. > Thanks in advance for your help. > > Best regards, > > Valerio Chiarini > > Il 2025-02-12 21:06 Eric Pettersen via Chimera-users ha scritto: >> Hi Valerio, >> I should preface things by saying that this script would be >> considerably easier to write in ChimeraX, because in ChimeraX the >> "runCommand" equivalent actually returns results from the command >> instead of nothing. So in ChimeraX you can directly determine if the >> clash-finding command actually found any clashes. >> So clearly the body of your 'if' statement never executed since it >> includes illegal statements that would have produced errors if the >> body of the 'if' statement had been executed, whereas you got no >> output. So the first thing is put "print file_names" right after the >> line that sets files_names and see if any of the file names contain >> your search string ("xxx"). If none of them do, then you need to >> figure out why: is folder_path wrong?; is search_string wrong?; do the >> files not end in .pdb?; etc. >> In addition, I can see some problems even if the 'if' statement body >> had executed. You don't close the models at the end, so they will >> build up and "findclash" will find more and more clashes. Your actual >> findclash command needs to be "findclash #0 test self". There is no >> "chimera.clashClashList". Probably the simplest way to determine if >> clashes were found is checking if the clashes pseudobond group has any >> pseudobonds in it. You can do that with: >> for m in chimera.openModels.list(hidden=True): >> if getattr(m, 'category', None) == "contacts": >> clashes_found = len(m.pseudoBonds) > 0 >> break >> --Eric >> Eric Pettersen >> UCSF Computer Graphics Lab >>> On Feb 12, 2025, at 2:23 AM, valerio chiarini via Chimera-users >>> <chimera-users(a)cgl.ucsf.edu> wrote: >>> Dear Responsible, >>> I am working on a script that should iterate through several >>> structures, check the structures for clashes among all atoms, and >>> eliminate the pdb in any clashes are found. >>> Here is what I have worked out so far: >>> # -*- coding: utf-8 -*- >>> import os >>> from chimera import runCommand as rc >>> from chimera import replyobj >>> import chimera >>> # Specify folder >>> folder_path = "/gporq3/store_0/usr/chiarini/chroma/chroma/" >>> # String to be found >>> search_string = "xxx" >>> # List of files in the folder >>> file_names = [fn for fn in os.listdir(folder_path) if >>> fn.endswith(".pdb")] >>> print("File trovati nella cartella:" + str(file_names)) >>> # Loop on every file containing 'search_string' in the name >>> for pdb_file in file_names: >>> if search_string in pdb_file: >>> pdb_path = os.path.join(folder_path, pdb_file) >>> # Open the PDB >>> rc("open {}".format(pdb_path)) >>> # Calculates clashes >>> rc("findclash") >>> rc("wait") >>> # Verify if any clashes are found >>> clashes = chimera.clashClashList() >>> if clashes: >>> # If clashes are found eliminates the file >>> os.remove(pdb_path) >>> print("Clash trovati, il file {} è stato >>> eliminato.".format(pdb_file)) >>> else: >>> # If no clash, exit normally >>> print("Nessun clash trovato per {}.".format(pdb_file)) >>> But no analisys is done at all. I have been searching through the >>> script page (https://www.rbvi.ucsf.edu/trac/chimera/wiki/Scripts) in >>> order to found some clue on this function but so far I have found >>> none. >>> Could you help me on this issue? >>> Thank you in advance >>> Valerio Chiarini _______________________________________________ >>> 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/ >> _______________________________________________ >> 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/ > > -- > Dr. Valerio Chiarini > > _Senior Scientist_ > > Proteins & Monoclona Antibodies Department – Takis Biotech > > c/o Tecnopolo > > Via di Castel Romano, 100 > > 00128 Rome, Italy > > Tel.: +39 06-50576077 > > Fax: +39 06-50576710 > > Email: chiarini(a)takisbiotech.it > > Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.takisbiotech.it&d=D… > > D_.lgs. 196/03_ > > _Le informazioni contenute in questa comunicazione e gli eventuali > documenti allegati hanno carattere confidenziale, sono tutelate dal segreto > professionale e sono ad uso esclusivo del destinatario. Nel caso questa > comunicazione Vi sia pervenuta per errore, Vi informiamo che la sua > diffusione e riproduzione è contraria alla legge e preghiamo di darci > prontamente avviso e di cancellare quanto ricevuto. __Grazie._ > > _This e-mail message and any files transmitted with it are subject to > attorney-client privilege and contain confidential information intended > only for the person(s) to whom it is addressed. If you are not the intended > recipient, you are hereby notified that any use or distribution of this > e-mail is strictly prohibited: please notify the sender and delete the > original message. __Thank you._ >

1 0

Bundle development for chimeraX - svg onClick event to run command from QWebEngineView
by Lou Holland 18 Feb '25

18 Feb '25

Hello, Apologies if this is the wrong email address to contact about this. I am currently working on a privateer bundle for carbohydrate validation in chimeraX. At present, I have it so that the privateer tool will display SNFGs of glycans present in the structure using svgs displayed in a QWebEngineView(). I would like, if possible, on clicking elements of the svg to run a chimeraX command (view /chainID:resID) to centre the view window on the residue in question. At present, I can implement an onClick event to display the command that should be run, but haven't managed to figure out how to just run the command from within that QWebEngineView. Is there a mechanism already in place for doing something like this that I could take advantage of? I'd considered using the "log html" to display the svgs in the log instead of the WebEngineView() so that I could take advantage of the href="cxcmd" functionality, but the svgs are long, with semicolons and new-line characters which interfere with this. Best wishes, Lou Holland (Pronouns: they/them) Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK

3 3

Assistance with ChimeraX Syntax for SPRITE Hands-On Module
by Zeenat Bashir 18 Feb '25

18 Feb '25

Dear ChimeraX Developers, I hope this email finds you well! I am currently developing a hands-on module for my students on visualizing SPRITE results using ChimeraX. However, I am facing an issue with the syntax for aligning the residues of *2HNT* with *1A0J*. The module I am using, which was provided by Basil (attached with this email), includes syntax for Chimera (refer to Figures 10 and 11 in the attached document). I have tried adapting the syntax for ChimeraX but have not been successful. I would really appreciate your guidance on this matter or if you could direct me to someone who might be able to assist in generating the correct command line syntax. Thank you so much for your time and help! Zeenat -- *Dr. Zeenat Bashir* *Senior Lecturer* *Biotechnology Lab Coordinator* *Department of Chemical and Biomolecular Engineering* *University of Pennsylvania* *310 Towne Building* *220 S. 33rd Street* *Philadelphia, 19104 -6393* bashirz(a)seas.upenn.edu

2 1

Roll command for multi objects in grid
by Enrico Martinez 18 Feb '25

18 Feb '25

Dear ChimeraX users! Using til command I split six superimposed structures, displaying them as the 2x3 table and then rotate each object along its axis within each grid using "roll" in the following way: # for 6 different object roll models #1 center #1 & protein roll models #2 center #2 & protein roll models #3 center #3 & protein roll models #4 center #4 & protein roll models #5 center #5 & protein roll models #6 center #6 & protein Would it be possible to simplify this to one "roll" command that will automatically rotate all displayed objects in the separate grids along its axis ? Many thanks in advance Enrico

2 3

Questions about match and view commands
by Enrico Martinez 16 Feb '25

16 Feb '25

Dear ChimeraX users! I am performing a visualization of the ensemble of conformers for the same protein defined in the chimerax as models #1 to #6. Here are some of my questions: 1 - I try to superimpose all structures to the first model using match #2-5 to #1 is it possible to use some regular expression instead of #2-5 to select all models from the second to the last e.g. to superimpose all structures to the first one in the script. 2 - I try to automatically orient the superimposed models along its principal axe in one command e.g. using view orient but it does not produce a proper orientation. What kind of trick could work for a nanobody object to orient it automatically e,g, along Z ? Many thanks in advance Enrico

3 6

assistance on bundle writting
by Nguyen, Catherine 14 Feb '25

14 Feb '25

Hello, I was hoping to get your help. I am trying to write a bundle and I am struggling to figure out how I can add psuedo-bonds using python as I want to connect two amino acids by the CA. Would you be able to help me find a way to do this? I hope to hear from you soon, Best wishes, Catherine

2 6

MUNKI Managed Software Download URL
by Antony Nelson 14 Feb '25

14 Feb '25

Hi, I appreciate this might seem an odd request, but do you have a public download location for ChimeraX software? There exists a widely used system by which administrators of Apple computers distribute software to their users by means of applications known as Munki and Autopkgr. Software which can be downloaded from public websites can be managed in such a way that new releases and updates are automatically added to the software repository Apple administrators curate for their users. Without making this publicly available, admins will only update your software when users request the admins to do so. Looking back on the Loupe Browser instances that have been made available to my users, they have only had access to versions: 0.8.0 0.9.0 0.9.1 0.93.0 1.1.1 1.7.1 and today they will have 1.9.0 If your software was made available via public download by a predictable URL, then they would have had access to every version released on the day it was added to your website since it was first requested by users. If you are concerned about the acceptance of terms of conditions then perhaps this could be incorporated into the URL string. Regards

2 1

How to get different silhouette widths for 2 maps
by Hong ZHAN 13 Feb '25

13 Feb '25

Hi there, I am trying to create a video with two maps overlay with different silhouette widths. It is easy to do with 2 images, but how I can do it in a video setting? If I change the width to 6, all maps changes the width to 6. Thanks! -Hong

3 4

Unable to load scripts at startup
by Pranav Shah 13 Feb '25

13 Feb '25

Hi Team, (I accidentally sent this to ChimeraX-bugs, copying it again here) I am trying to load some scripts at startup via the chimerax_custom_functions.cxc command file - open /Users/ps/.chimerax/chimerax_commands/chimerax_custom_functions.cxc in the log file I see the following message: still retrieving bundle list from toolshed open /Users/ps/.chimerax/chimerax_commands/chimerax_molmap_cube.py Error running startup command 'open /Users/ps/.chimerax/chimerax_commands/chimerax_custom_functions.cxc': Unknown command: open /Users/ps/.chimerax/chimerax_commands/chimerax_molmap_cube.py This is strange as simply running "open /Users/ps/.chimerax/chimerax_commands/chimerax_molmap_cube.py" in the ChimeraX command panel runs perfectly fine! the error occurs only when I try to run that line through the .cxc file. Am I missing something? or could this be a bug? I am on the stable release of ChimeraX (version 1.9). 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

3 3

PAEcontacts colorkey
by ccinsua＠gmail.com 13 Feb '25

13 Feb '25

Hi all, Thank you very much for your work with chimerax. I've been using it to study alphafold complex prediction, and I find the command alphafold contacts very useful. The default color key (guess it is paecontacts, according to documentation) ranges are blue (low PAE) - green (medium PAE) - yellow (high PAE). However, I am unable to add a color key using "key paecontacts". Somehow I have to define it myself. Is there anything I am missing? I would like to stick to the blue-green-yellow scheme. Thanks a lot in advance Carlos

1 1

NASA - Country of Origin Statement and 508 Conformance Request: UCSF ChimeraX
by Price, Dru C. (LARC-B730)[eMITS] 12 Feb '25

12 Feb '25

Hello, my name is Dru and I work for the NASA Commercial IT Acquisition Team. As such, I ensure that all NASA acquisitions of Covered Articles comply with Title II; General Provision Section 208 and Title V; General Provisions Section 514 of the Consolidated Appropriations Act, 2021, Public Law 116-260<https://www.congress.gov/bill/116th-congress/house-bill/133/text>, enacted December 27, 2020. To do so, the Country of Origin (CoO) information must be obtained from the company that develops, produces, manufactures, or assembles the product(s). Please specifically identify the country, or countries, in which each of the following software products is developed and maintained: * UCSF ChimeraX Additionally, if available, please identify all authorized resellers of the product(s) in question. Finally, I am requesting an Accessibility Conformance Report (starting from Page 10 of the attached VPAT) be completed and returned so that NASA can assess the product's level of 508 Conformance. More information regarding Section 508 of the Rehabilitation Act of 1973 and what it means to manufacturers/developers can be found at https://www.section508.gov/sell/vpat. I have attached a blank copy of the latest revision of the VPAT standard if you do not already have a completed VPAT available for this product. Please complete this document to the best of your abilities, if one is not already available. Product / Service Description Model Number Country of Origin Is final testing performed in the United States? Please let me know if you have any questions. Thank you, Dru C. Price Procurement Analyst eMITS | [ROTHE ARES JV] Commercial IT Management Support Croscutting Agency Service (CAS) Branch Enterprise Business Management Office (EBMO) NASA - Office of the Chief Information Office (OCIO) [cid:image001.png@01DB7D5D.40BD4D20]<https://teams.microsoft.com/l/chat/0/0?users=dru.c.price@nasa.gov> [cid:image002.png@01DB7D5D.40BD4D20]

3 3

ChimeraX fetch by PubChem CID
by Elaine Meng 12 Feb '25

12 Feb '25

> On Feb 12, 2025, at 11:41 AM, Alexander Mansueto <alexander.j.mansueto(a)vanderbilt.edu> wrote: > > Can we import pubchem CID molecules to model proteins with lipids? Would be very cool. Hi Alexander, The recommended address for asking ChimeraX questions is the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> mailing list CC'd here, see "contact us" on our website or in the ChimeraX menu: <https://rbvi.ucsf.edu/chimerax/docs/contact.html> If PubChem Compound has the coordinates, you can open them in ChimeraX by CID, e.g. command open pubchem:12123 - OR - open 12123 from pubchem ... as explained here <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> ...or with menu: File... Fetch by ID, choosing the Pubchem option and specifying the CID in the dialog: <https://rbvi.ucsf.edu/chimerax/docs/user/fetch.html> However, not every entry in PubChem Compound has coordinates available, so I don't know if it will work for your specific molecules of interest. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Get color code of a custom color
by Ahmad Khalifa 11 Feb '25

11 Feb '25

I created a custom color that I want to use in a different session. is there a way to do that besides trying to match colors by eye? Regards.

5 4

steam VR running but still get an error with Vr on command.
by Krishnan Raman 10 Feb '25

10 Feb '25

[cid:5bbc0381-58d6-4058-bc7c-183bcd144645] Steam VR is running and still i get this error. Am i overlooking something? thanks Krish CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

2 1

there is no amination？？？
by 刘涛 07 Feb '25

07 Feb '25

2 2

Recording MD Trajectory Movie in ChimeraX
by Gourav Das 07 Feb '25

07 Feb '25

Dear ChimeraX users, I have performed MD simulation of a system using AMBER20. The topology and trajectory files are in .parm7 and .nc formats, respectively. I would appreciate your guidance on visualizing and recording the trajectory as a movie in ChimeraX. Thank you for your support. With regards, Gourav Das Research Scholar Department of Chemistry Indian Institute of Technology Kharagpur West Bengal, India-721302 Mob: +91-6295251060 --

2 5

Double and Triple Bond Stick Style
by Smith, Chase 05 Feb '25

05 Feb '25

Dear ChimeraX, I was just wondering why there is no way to represent a double or triple bond in either the ligands or the protein amino acids when viewing as a Stick or Ball-and-Stick representation? I sometimes use Chimera or ChimeraX to make visuals for my lectures, and the students often have difficulty in understanding due to the absence of the multiple bonds. I would love to have the ability to represent the double or triple bonds with multiple lines between the atoms. Thank you, Chase Smith ... ChaseSmith, PhD Chair, Department of Pharmaceutical Sciences & Associate Professor of Medicinal Chemistry School of Pharmacy MCPHS University 19 Foster Street | WorcesterMA01608 T 508.373.5717F 508.890.5618C 978.855.7203 chase.smith(a)mcphs.edu www.mcphs.edu MCPHS University Confidentiality Note: This e-mail, and any attachment to it, is intended to be confidential and might be legally privileged. It is intended solely for the use of the addressee. If you are not the intended recipient, you are hereby notified that reading, copying, disseminating or distributing this email is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.

5 5

Re: Introduction of a proteolytic cleavage in ChimeraX
by Elaine Meng 04 Feb '25

04 Feb '25

> On Feb 4, 2025, at 3:30 AM, Mark Hilge <markhilge(a)icloud.com> wrote: > > Dear Dr. Meng, > [... details removed ...] > Question: In ChimeraX, is there a possibility to introduce a proteolytic cleavage between say Leu112 and R113? This should result in Leu112 with a carboxylate group followed by a TER keyword. > > Many thanks in advance! > Kind regards, > Mark Dear Mark, It depends what you want to use this for. If it's just for a figure, that is totally different than if you were going to do some extensive workflow afterwards. If you have an input PDB file, one "dumb" way is to text-edit it to put the TER card in before opening in ChimeraX. However, that will not add a carboxylate oxygen, there would just be a dangling C=O. If you wanted an OXT you would have to add it "manually," e.g. in the Build Structure tool. However, that will be problematic because it won't want to add the OXT right on top of the N, which is where it would want to go. You'd also have to change the conformation of the chain, e.g. rotate a bond with the mouse mode or the "torsion" command. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html> Within ChimeraX, you could use command ~bond to remove bonds. However, if you do this within a chain defined in the input (e.g. PDB SEQRES lines or mmCIF file equivalent), it will then draw a dashed line because it still "knows" they are supposed to be connected within the chain because of the SEQRES records in the PDB file. <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html> So it's all more complicated than you might think, especially if you wanted everything to be correct for some subsequent modeling workflow. You might instead give the two parts two different chain IDs. One way is to text-edit the PDB file. Another is to open the thing twice, delete the first part of the chain in one copy, delete the other part of the chain in the other copy, and then use "combine" to create a new model that has both parts but with different chain IDs, and then use "save" to save a PDB file of that combined model. <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> However, you would still need to text-edit the PDB file manually so that there are SEQRES records for the two different chains (the two parts of the original single chain) that each contain only the residues for the corresponding part. These are different than the ATOM records that have the coordinates. And I can't even begin to explain how you might do it in mmCIF, all of this is in PDB format only. So if you bothered to do all that, then if you use "addh" it will automatically add the "OXT" because it will finally recognize the new cleaved C-terminus as a real C-terminus. <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/addh.html> For future reference: please use chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address CC'd here to ask questions about ChimeraX, omitting any information that needs to remain private. If you send email to me only, it may not get answered. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Suppress errors when using runscript?
by Vorländer,Matthias Kopano 03 Feb '25

03 Feb '25

Hi, I wondered if it is possible to suppress/ignore an error message when executing scripts with runscript. Specifically, I have a script to analyze alphafold (3) predictions and select residue interfaces residues using the interface select command. The selection for each of the five model is then saved in a named selection: # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection for the interface residues. name frozen interface_residues$2_model_4 sel This works fine when all models show contacts , however, if one of the models/predictions does not have any residues involved in an interface, the script stops with the error “Nothing is selected by the specifier”. It would be great if the script does not pause at this message. Below the full .cxc script I am using: Best, Matthias # Generate AF contacts for all predictions of an AF3 run # # Usage: # runscript analyse_af3_prediction.cxc <AF_screen_directory> <custom_prediction_name> # The script assumes that five models were generated by AF. It expects the CIF files to be in a sub‐directory # matching the pattern "*model_X*.cif" and the corresponding JSON files in a sub‐directory matching "*data_X*.json" # for each model number X (4, 3, 2, 1, 0). # For the alignment and mseries slider command to work properly, the script assumes no other models are open. echo "Usage: runscript analyse_af3_prediction.cxc <AF_screen_directory> <custom_prediction_name>" ##### Model 4 ##### # Open the structure and its JSON scores for model 4. open $1/*model_4*.cif open $1/*data_4*.json structure last-opened hide show c # Generate AF contacts (using JSON scores) for chain A (or the first chain) alphafold contacts last-opened &/A name model_4_af_contacts_$2 # Create pseudobonds for the contacts and label them with residue names and numbers. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Save the pseudobond representation to a file. save $1/af_contacts_model_4_$2.txt format pseudobonds sel true echo "AlphaFold contacts (derived from JSON file) saved to $1/af_contacts_model_4_$2.txt" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection for the interface residues. name frozen interface_residues$2_model_4 sel show interface_residues$2_model_4 style interface_residues$2_model_4 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_4 saveFile $1/interface_residues$2_model_4_buriedArea_300.txt # Color the model for clarity. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_4 and info saved to $1/interface_residues$2_model_4_buriedArea_300.txt" ##### Model 3 ##### # Open the structure and its JSON scores for model 3. open $1/*model_3*.cif open $1/*data_3*.json structure last-opened hide show c # Generate AF contacts. alphafold contacts last-opened &/A # Create pseudobonds and label them. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Save the pseudobond representation. save $1/af_contacts_model_3_$2.txt format pseudobonds sel true echo "AlphaFold contacts (derived from JSON file) saved to $1/af_contacts_model_3_$2.txt" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection. name frozen interface_residues$2_model_3 sel show interface_residues$2_model_3 style interface_residues$2_model_3 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_3 saveFile $1/interface_residues$2_model_3_buriedArea_300.txt # Color the model. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_3 and info saved to $1/interface_residues$2_model_3_buriedArea_300.txt" ##### Model 2 ##### # Open the structure and its JSON scores for model 2. open $1/*model_2*.cif open $1/*data_2*.json structure last-opened hide show c # Generate AF contacts. alphafold contacts last-opened &/A # Create pseudobonds and label them. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Save the pseudobond representation. save $1/af_contacts_model_2_$2.txt format pseudobonds sel true echo "AlphaFold contacts (derived from JSON file) saved to $1/af_contacts_model_2_$2.txt" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection. name frozen interface_residues$2_model_2 sel show interface_residues$2_model_2 style interface_residues$2_model_2 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_2 saveFile $1/interface_residues$2_model_2_buriedArea_300.txt # Color the model. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_2 and info saved to $1/interface_residues$2_model_2_buriedArea_300.txt" ##### Model 1 ##### # Open the structure and its JSON scores for model 1. open $1/*model_1*.cif open $1/*data_1*.json structure last-opened hide show c # Generate AF contacts. alphafold contacts last-opened &/A # Create pseudobonds and label them. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection. name frozen interface_residues$2_model_1 sel show interface_residues$2_model_1 style interface_residues$2_model_1 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_1 saveFile $1/interface_residues$2_model_1_buriedArea_300.txt # Color the model. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_1 and info saved to $1/interface_residues$2_model_1_buriedArea_300.txt" ##### Model 0 ##### # Open the structure and its JSON scores for model 0. open $1/*model_0*.cif open $1/*data_0*.json structure last-opened hide show c # Generate AF contacts. alphafold contacts last-opened &/A # Create pseudobonds and label them. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Save the pseudobond representation. save $1/af_contacts_model_0_$2.txt format pseudobonds sel true echo "AlphaFold contacts (derived from JSON file) saved to $1/af_contacts_model_0_$2.txt" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection. name frozen interface_residues$2_model_0 sel show interface_residues$2_model_0 style interface_residues$2_model_0 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_0 saveFile $1/interface_residues$2_model_0_buriedArea_300.txt # Color the model. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_0 and info saved to $1/interface_residues$2_model_0_buriedArea_300.txt" ##### Final Steps ##### # Move all models (except the last-opened) to a common group (optional) mm #*&~last-opened&/A to last-opened&/A # Create an mseries slider for the five models. mseries slider #1-5 title $2 name $2_slider mseries #1-5 echo "Use the slider to go through the models!" echo "Pairwise contacts (based on the JSON fle) and all residues involved in an interface (based on a buried surface are of 300 Angstrom or more) have been saved in the input folder for each prediction" echo "You might want to increase stringency by calcualting the overlap between all predictions"

2 1

Getting two color keys in the same ChimeraX session
by Elaine Meng 03 Feb '25

03 Feb '25

> Begin forwarded message: > > From: Eric Pettersen via Chimera-users <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] Re: key command > Date: February 3, 2025 at 11:52:12 AM PST > To: Fabian Glaser <fglaser(a)technion.ac.il> > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Reply-To: chimera-users(a)cgl.ucsf.edu, Eric Pettersen <pett(a)cgl.ucsf.edu> > > Hi Fabian, > There is no direct support for multiple keys, but it is pretty easy to “trick” ChimeraX into showing multiple keys. You would create your first key normally, getting it exactly the way you want it to look before creating the next key. You create the next key with the following Python code: > > from chimerax.color_key.model import ColorKeyModel > m = ColorKeyModel(session) > > If the above was in a file ending in ‘.py’, you could just use the ‘open’ command to run it and create the key. I’ve attached a file with that code in it for convenience. Once you have created the key, then all operations that affects keys (like the ‘key’ command) will affect the new key and leave the original key as is. If you had the Color Key tool up, it will continue to show the old values. Just close it and re-open it to show the new values. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > >> On Feb 3, 2025, at 6:31 AM, Fabian Glaser via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >> >> Hi, >> >> We would be interested to add more than one key color bar in the same chimerax session. But we noticed the key command allows only one color key can be present at a time. >> >> Is there a way to add more than one color key in the same session? >> >> Thanks a lot, >> >> Fabian >> >> >> Fabian Glaser, PhD >> >> Technion Centre for Structural Biology (TCSB), Computational Section, Head >> Technion Human Health Initiative (THHI) >> Technion - Israel Institute of Technology, Haifa, Israel >> fglaser(a)technion.ac.il >> +972 (0)48293701 >> >> >> >> _______________________________________________ >> 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/ > > _______________________________________________ > 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/

1 0

Grid mode and multiple viewports
by Roden Deng Luo 03 Feb '25

03 Feb '25

Hi, I find there is a `tile` command. After I enter the tile mode, the zoom is global. I guess `tile` is implemented by transforming the active models in the global scene explicitly. I wonder if there is a way to have the zoom independent for each model, similar to the grid mode in PyMol. A further question, more from a developer's perspective, is whether having multiple 3D rendering viewports in ChimeraX is possible. I imagine each viewport can have its own active models in the scene and its own camera. Different cameras and other operations might be synced upon users' request. This video (https://youtu.be/7KZ1P-nPav8?si=Z1hiBBuRiWop2WFC) demos the feature (in an old version of Houdini). Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

4 8

aligning maps generated by chimeraX
by msteves＠berkeley.edu 31 Jan '25

31 Jan '25

Hello, I'm new to Chimera, but would like to use it to generate surface maps of electrostatic potential and hydrophobicity, then output for further analysis. I've generated maps using coulombic and mlp commands, and successfully saved these to .MRC format. However, when I go and read these files, the dimensions of the maps are different, so I'm not sure how to properly overlay these maps in my later analysis. Is there a way to have Chimera generate maps only within a given spatial range, so I end up with maps of the same size? Or another way you would recommend going about this? In later analysis I'd also like to make use of the SAS calculated by Chimera, and I imagine I will also have difficulties properly aligning the surface to the maps, so any advice on this would also be greatly appreciated! Thanks, Megan Steves

2 1

Question about Surface Volume Overlap Calculation
by John Watters 31 Jan '25

31 Jan '25

Hello, I was wondering if anyone had any tips/tricks/useful functions for quantifying the volume of the overlap between two surfaces in ChimeraX? I am looking specifically to make a metric to compare steric clashes of molecules in different orientations. Thank you for any help you can provide! Best, John

3 4

Add help for reusable ChimeraX script that takes command line arguments?
by Vorländer,Matthias Kopano 30 Jan '25

30 Jan '25

Hi, It’s me again 😉 I wondered how I can add a help page to a re-usable ChimeraX script that is run via runscript. I saved the following script in my ChimeraX presets: #Required arguments: first is the uniprot ID, second is the model ID that will be used for mapping! alphafold fetch $1 #get the missense data open $1 fromDatabase alpha_missense format amiss #associate missense data to structure mutationscores structure $2 #label each residue with matric mutationscores label #1 amiss height 3 #define a new score called avg by avergaing over all substitution scores mutationscores define avg fromScore amiss setAttribute true combine mean #color by avg missense score color byattribute r:avg $2 target csab palette palette bluered range full #scale cartoon by acg missense score cartoon byattribute r:avg #!$2 and then defined an alias in my startup commands so I don’t need to type the full path alias map_missense runscript /Users/matthias.vorlaender/Documents/ChimeraX_presets/map_missense.cxc $1 $2 Is there a way to display the expected user inputs when the script is called without arguments? Cheers, Matthias

2 3

Feasibility of selecting chain ID via uniprot ID?
by Vorländer,Matthias Kopano 30 Jan '25

30 Jan '25

Hi again : ) When comparing structures from different sources (such as different PDB depositions, or an Alphafold structure), it is always tedious to figure out which chain belongs to which protein (especially for large structures like spliceosomes) for consistent coloring or alignment. I wondered if it would be technically feasible to use the uniport ID to match a specific chain directly, since the association between chain ID and uniport ID should be present at least in structures from curated databases such as the PDB and Alphafold. So the ambition would be to be able to use ‘color IF4A3_HUMAN red’ directly, without having to look chain IDs. An added bonus would be to be able to skip the species identifier, in case you have models containing IF4A3_MOUSE and IF4A3_HUMAN, and match both with IF4A3 …. Would be curious to hear your thoughts. Thanks a lot, and best wishes, Matthias

3 3

Encode: saving a movie on a Windows laptop, and colouring residues in the multiple sequence
by Anne-Frances Miller 30 Jan '25

30 Jan '25

Dear ChimeraX My class is having a blast with this! I have assigned the class to make a movie, based on the morph and encode commands. On Macs, your instructions are flawless. However I have students using Windows10 and Windows 11. For these, could you please provide an example movie encode command including path and good choice of format please? Also, when I open a multiple sequence alignment in ChimeraX, is there a way to apply Taylor or other colouring to the MSA? This used to be possible in Chimera's MAV. Thank you, Anne-Frances Novel Meritorious Research (and teaching) —•—•—•—•—•—•—•—•—•—•—•—•—•— A.-F. Miller, Ph. D. (she/elle/sie) Distinguished Prof. of Arts and Sciences Professor of Chemistry University of Kentucky https://uky.zoom.us/j/3250841836 https://millerlablive.wordpress.com/ Visiting Fellow, Einstein Foundation of Berlin

3 4

Possible to plot attribute value over sequence?
by Vorländer,Matthias Kopano 29 Jan '25

29 Jan '25

Dear ChimeraX team, I wondered if it is possible to generate a line or scatter plot of an attribute value (B factor, Alphafold pLDDT scores, or AlphafoldMissense score…) over the residue number? For example something like this (taken from https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0089116) : [cid:image001.png@01DB7242.B1C3F8A0] Specifically, for the AlphafoldMissense data, such a plot would be more informative then the default histogram that is displayed when fetching the scores when looking for functional hotspots in your POI. Many thanks, MAtthias

3 5

Chai discovery data
by Reza Salavati, Prof. 29 Jan '25

29 Jan '25

Hello, I have downloaded the Chai discovery data in .npy and .json file formats. How can I open these files in Chimera X? Thank you Reza

4 4

ChimeraX installation on Debian Trixie? (Unsatisfied dependencies)
by Francisco Murphy Pérez 29 Jan '25

29 Jan '25

``` root@debian# apt install ./ucsf-chimerax_1.9ubuntu24.04_amd64.deb Note, selecting 'ucsf-chimerax' instead of './ucsf-chimerax_1.9ubuntu24.04_amd64.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: Unsatisfied dependencies: ucsf-chimerax : Depends: libgdk-pixbuf2.0-0 but it is not installable root@debian# apt install ./libgdk-pixbuf-2.0-0_2.42.12+dfsg-1+b1_amd64.deb Note, selecting 'libgdk-pixbuf-2.0-0' instead of './libgdk-pixbuf-2.0-0_2.42.12+dfsg-1+b1_amd64.deb' libgdk-pixbuf-2.0-0 is already the newest version (2.42.12+dfsg-1+b1). libgdk-pixbuf-2.0-0 set to manually installed. Summary: Upgrading: 0, Installing: 0, Removing: 0, Not Upgrading: 0 ``` From here https://github.com/RBVI/ChimeraX/blob/develop/mkubuntu.py (line 308) looks like "libgdk-pixbuf2.0-0": "2.40.0+dfsg", is missing a dash?

2 1

Re: [Chimera-users] How to subgroup the chains of oligomer pdb
by Elaine Meng 28 Jan '25

28 Jan '25

Hello, If you are asking about ChimeraX, it is better to use the address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here, instead of the older Chimera address. I don't know if this is exactly what you want but you can give a name to any set of atoms. For example, open your-oligomer.pdb name frozen mygroup1 #1/A-F name frozen mygroup2 #1/G-L select mygroup1 color mygroup2 orange See ChimeraX "name" command (your name can be something else, like gp20 instead of mygroup1): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html> Or, a totally different thing you could do is split the model into two different models, for example, open your-oligomer.pdb split atoms #1/A-F atoms #1/G-L That would make your model #1 into two separate models #1.1 and #1.2 with the specified sets of atoms. See ChimeraX "split" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html> You can also change names of models (what is shown in the Models list) using the "rename" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 24, 2025, at 8:14 PM, sktewary via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Friends > > I would like to learn how to subgroup the chains of a oligomer pdb. suppose i have a pdb with chain A to L, in which A,B,C,D,E,F belongs to gp20 and G,H,I,J,K,L belongs to gp20. My question is how to add the descriptions to these groups chains so that when the viewer look the pdb file when he selects the gp20 all the chains to this group are selected A-F. > > Please give your feedback if chimerax can do it, how to do it?

2 1

Limit blast search to species
by Vorländer,Matthias Kopano 28 Jan '25

28 Jan '25

Dear ChimeraX team, I wondered if it is possible to limit a BLAST search to only a single species when querying a selected database. This would facilitate identifying homologs in your favorite model organism, rather than picking up the most closely related homolog overall (i.e when using the alphafold database). Many thanks, Matthias

3 7

Clustal alignment
by Rosaleen Calvert 28 Jan '25

28 Jan '25

Hi. Apparently alignment is newly available in Chimerax 1.9. I cannot find how to do this in Tools: sequence or Tools: structure analysis. From Rosy Calvert

2 1

movie crossfade
by Enrico Martinez 27 Jan '25

27 Jan '25

Dear ChimeraX users! I am recording a short animation demonstrating my docking ensemble # start recording movie record ## play DOCKING movie from end to begining coordset #1 96,1,-1 wait 96 Would it be possible to add a smooth transition between each frame (docking pose) using the movie crossfade command ? If so, how should this command be placed in the script ? Many thanks in advance ! Enrico

3 13

Fwd: ChimeraX installation on Debian Trixie? (Unsatisfied dependencies)
by Eric Pettersen 27 Jan '25

27 Jan '25

Greg, I’m guessing this is yours… —Eric > Begin forwarded message: > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Fwd: [chimerax-users] ChimeraX installation on Debian Trixie? (Unsatisfied dependencies) > Date: January 23, 2025 at 3:45:29 PM PST > To: chimerax-programmers(a)cgl.ucsf.edu > Cc: Elaine Meng <meng(a)cgl.ucsf.edu> > > Anybody? > >> Begin forwarded message: >> >> From: Francisco Murphy Pérez via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> >> Subject: [chimerax-users] ChimeraX installation on Debian Trixie? (Unsatisfied dependencies) >> Date: January 19, 2025 at 1:22:00 PM PST >> To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> >> Reply-To: Francisco Murphy Pérez <francisco.murphy(a)ibt.unam.mx> >> >> ``` >> root@debian# apt install ./ucsf-chimerax_1.9ubuntu24.04_amd64.deb >> Note, selecting 'ucsf-chimerax' instead of './ucsf-chimerax_1.9ubuntu24.04_amd64.deb' >> Some packages could not be installed. This may mean that you have >> requested an impossible situation or if you are using the unstable >> distribution that some required packages have not yet been created >> or been moved out of Incoming. >> The following information may help to resolve the situation: >> >> Unsatisfied dependencies: >> ucsf-chimerax : Depends: libgdk-pixbuf2.0-0 but it is not installable >> >> root@debian# apt install ./libgdk-pixbuf-2.0-0_2.42.12+dfsg-1+b1_amd64.deb >> Note, selecting 'libgdk-pixbuf-2.0-0' instead of './libgdk-pixbuf-2.0-0_2.42.12+dfsg-1+b1_amd64.deb' >> libgdk-pixbuf-2.0-0 is already the newest version (2.42.12+dfsg-1+b1). >> libgdk-pixbuf-2.0-0 set to manually installed. >> Summary: >> Upgrading: 0, Installing: 0, Removing: 0, Not Upgrading: 0 >> ``` >> >> From here https://github.com/RBVI/ChimeraX/blob/develop/mkubuntu.py (line 308) looks like "libgdk-pixbuf2.0-0": "2.40.0+dfsg", is missing a dash? >> >> >> _______________________________________________ >> 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/ >

1 0

ChimeraX question - Diana Mayorga
by Diana Carolina Mayorga Gonzalez 27 Jan '25

27 Jan '25

Hi, Hope you are well. I would like to know if I can do these transparent bubbles in ChimeraX showing the atoms stick as well. If it is possible, could you help me with a small tutorial, please? [cid:add7b0b3-f091-48a9-bc44-329473b06f2e] Thank you so much in advance, Diana Carolina Mayorga G PhD Student Yannick Doyon Lab Research Center - Université Laval Department of Reproduction, mother and youth health (RSME) Québec, Canada

2 1

Re: movie with model label/name
by Elaine Meng 26 Jan '25

26 Jan '25

Dear Saif, To ask questions in the future, we recommand that you please use the mailing list for the appropriate program (chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> for Chimera, chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> for ChimeraX). If you mail me individually your question may not get answered. I will answer for ChimeraX since that is our preferred program now -- Chimera is no longer developed. In general, this topic is covered in the ChimeraX "making movies" page: <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html> You can do all of this with a command script using several commands. There is a "morph" (atomic) or "morph maps" (density maps) command to do the morphing. You would probably change the display (colors, styles, etc.) to how you want it for your movie and then save a session. Then, to work on making a movie you would create a command script that applies to the session. The reason to save a session is so you can avoid redoing the same setup calculations, coloring, etc. every time you run the script. You can do all that stuff first and then save a session. Usually working on the script takes several days, so you would just restore your session and then continue working on the script. The script would contain what you actually want to show in the movie. You can play back an atomic morph with "coordset" and show/hide labels with "2dlabel" and you can do all kinds of other stuff as well, like zoom and rotate. You may also want to save positions in your session file (see "view" command) and then during the movie script, restore those different positions. When the movie script contains what you want to show in your movie, which is usually a long interative process after you play it back several times and keep changing the commands, then you would add the movie-recording commands (see "movie" command) to start recording at the beginning and save the movie file at the end. There are examples in our "making movies" page and links therein to the help for the commands mentioned above as well as movie-making tutorials. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 26, 2025, at 5:53 AM, Md Saiful Islam - MRC LMB <sislam(a)mrc-lmb.cam.ac.uk> wrote: > > Dear Elaine > Just wondering, is there any script to make movies to show the conformational changes between multiple models with the labeling of each of the models shown. > For example, I want to make a movie to show a morph between three cryoEM models where I want to label the three models while morphing from model 1 to model 2 and from model 2 to model 3. > > Accept my apologies if you already shared this before. > > Many thanks for your help. > > Kind Regards > Saif

1 0

Confirming coordinate axis
by Abhinaba Das 24 Jan '25

24 Jan '25

Dear ChimeraX-users, I'm writing to ask if there is a way to view the x,y,and z axis live while model building. I've a helical map generated in CryoSPARC which has a D1 symmetry. I could generate the asymmetric unit (ASU) for the corresponding C1 reconstruction but having issues applying D1 symmetry. The approach I've taken is to make a diheral copy of the C1 ASU (turn y 180 center <mapId> coordinateSystem <mapId> model <modelid>; followed by combine command). This should generate the dihedral ASU, and if the helical symmetry is applied should generate the symmetric copies (?). But seems not to be working.. I've assumed that the dyad axis is along the y-axis (cryosparc says for its output map). Just wondering if the axes are aligned.. Thanks, Abhi

3 2

openmmforcefields
by Lewandowski, Jozef 24 Jan '25

24 Jan '25

Hi, I really like that openmm is implemented in ChimeraX. Is it possible somehow to implement/include openmmforcefields (https://github.com/openmm/openmmforcefields)? Specifically, I often use custom residues and would love to, e.g. parametrise them using GAFF, to do some small local minimisation in ChimeraX. Or is there any way of passing force fields for ligands parametrised with GAFF to ChimeraX? Thanks, Józef

3 2

Surface Color
by Hansen, Bryan (NIH/NIAID) [E] 24 Jan '25

24 Jan '25

Hi, I'm having issues with coloring a surface by volume. When I compare the two volumes I don't get the larger volume completely colored and even when I set 'Color outside volume' to match the same color as the 0 value which in this case is the blue it still renders grey. Can you help me with which step I'm messing up? Thanks. Bryan Hansen Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU Rocky Mountain Laboratories 903 S. 4th St Hamilton, MT 59840 406.363.9202 *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************

2 3

Assigning a custom net charge for a ligand using dockprep
by Jade Shi 24 Jan '25

24 Jan '25

Hi, I am trying to use dockprep to prepare PDB files with ligand molecules for subsequent modeling and analysis. I am currently using the "dockprep" command with no additional arguments. However, I find that occasionally when calculating partial charges using antechamber/AM1-BCC, ChimeraX assigns an incorrect total charge to the ligand resulting in an incorrect charge distribution. Is there a way to specify this manually, i.e. the equivalent of supplying the -nc flag when using antechamber directly? Thanks a lot! Jade

2 1

Draw and build secondary structures interactively
by Roden Deng Luo 22 Jan '25

22 Jan '25

Hi, I know there is a tool and command "build". But it is not that interactive. I wonder if there is a feature in ChimeraX (or any other tools) that can allow the user to draw in 3D space (or 2D) lines and then specify some segments as alpha-helices and some other segments as beta-sheets. I imagine the generated structure can be a backbone populated with G (glycine). Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

2 2

"forEach" command to open multiple pdb from multiple directories and save images there ?
by Vincent CHAPTAL 21 Jan '25

21 Jan '25

Hi, I would like to open multiple alphafold results that are stored in several folders, make an image, and save the image in those orignial folders. I'm using the forEach command to open all the results and run the script to create an image, and it works very well: open script.cxc forEach /PATH*/ranked_*.pdb script.cxc: open reference-structure.pdb match #1 to #2 color #*/B green color #*/C red color #*/D blue view matrix camera 0.87509,0.019021,-0.48356,-124.35,0.48393,-0.035333,0.87439,694.49,-0.00044561,-0.99919,-0.040123,163.41 I'm only stuck at the saving process where I'd like to save an image ranked_*.png matching the original name and folder location: save /PATH*/$file.png doesn't work because the /PATH*/ is not recognized as an existing directory. save /$PATH*/$file.png gives the same error. If I remove the /PATH/ it saves all the images on top of each other and it defeats the purpose. Could you let me know how to save in the folder where the .pdb was read from? 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/

2 2

UCSF ChimeraX - Using the software for teaching
by Fernandes, Clive 17 Jan '25

17 Jan '25

Dear Team, Hope the new year is treating you well. I'm Clive Fernandes, working within the Technology Procurement Team at Imperial College London. A member of the teaching staff has contacted me to inquire whether they can use ChimeraX for teaching purposes. This would involve installing the software in a few small lab/teaching rooms. Could you please confirm if this use is permissible and does not violate the terms and conditions? Thank you. Best wishes, Clive Fernandes Software Asset Management Lead Information & Communication Technologies Level 4, Sherfield Building Imperial College London South Kensington London, SW7 2AZ Connect on LinkedIn<https://www.linkedin.com/in/clive-fernandes-/>

2 2

Regarding the issue of residue display
by 张馨丹四川大学生物治疗国家重点实验室 16 Jan '25

16 Jan '25

There are gaps between adjacent residues sticks and cartoons. How should this problem be solved? Looking forward to your reply. Thank you!

2 2

No command line or the right-side tap in ChimeraX1.9
by Chloe Chin 16 Jan '25

16 Jan '25

Hi, I'm an undergraduate student who just started to use ChimeraX! Unfortunately, I found that ChimeraX1.9 did not show any command line or the tap that should be shown in the right-side (where we can see the log). However, it appears when I use ChimeraX 1.10. Can anyone let me know what might be wrong? Also, will there be any problem if I just use ChimeraX 1.10 (or the daily build, because I downloaded the daily exe and it became 1.10)? My laptop is window 11 by the way. I'd appreciate it a lot if I could get an answer for my questions... I'll be waiting for the reply :) Best, Chloe

2 1

Different dihedral angle results between Chimera and ChimeraX
by Alexander Hung Lee 16 Jan '25

16 Jan '25

Hello, I was looking to calculate the dihedral angle, and ChimeraX was giving me a value that I didn't agree with. I ran the same command with the older Chimera, and it's more in line with what I expected I was looking at the dihedral angle for N-acetyl in sialic acid. ChimeraX gave me 6.9 degrees while Chimera gave me -179.95 degrees. Is there something wrong that I'm doing? It's from the same pdb file. [cid:d7d74402-46c4-4f1e-8ee1-2d78698cb88f] Regards, Alex

2 2

Question about the tool Find Cavities
by svle＠tiscali.it 16 Jan '25

16 Jan '25

Hi, the tool Find Cavities returns as information about each detected cavity the number of points describing the what has been found. It is possible to obtain the coordinate of that points so to calculate the "center" of a found cavity of interest? Thanks. Saverio

3 4

pb with alphafold error plot when we used dimer
by Jean-François Bureau 15 Jan '25

15 Jan '25

Hi, When I stimulate dimer using alphafold3, it is not possible to load the error plot since Chimerax is waiting to have the data of the first protein and find that of both. Best JF Bureau

2 1

Re: From the Correct email now: ChimeraX corrections for the getting started tutorial.
by Elaine Meng 13 Jan '25

13 Jan '25

Hi Anne-Francis, For ChimeraX, we don't have an exact parallel to the "getting started" tutorial for Chimera. However, the one I usually recommend as an intro to general molecular modeling (such as for a class) is Protein-Ligand Binding sites <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> You can also look down through the tutorials index to see if there are any more specific ones that might interest you. <https://www.rbvi.ucsf.edu/chimerax/tutorials.html> The ChimeraX "quick start" sections can be followed sequentially as they are written, but I understand it is not really the same kind of narrative as most tutorials. You may also be interested to try the "click to execute" approach where you don't even have to type the commands (although perhaps it does not provide as much reinforcement for the students to learn them). Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 12, 2025, at 7:01 PM, Anne-Frances Miller <afmill3r2(a)gmail.com> wrote: > > Oh shoot! > You are right, > > I see how that happened though, for the ChimeraX https://www.rbvi.ucsf.edu/chimerax/tutorials.html > I don't see any getting started guide that leads people though all the basics from start to finish with commands being introduced. > > Have you got such a thing yet? This class cannot use the quick start guide, they need a full work flow. > > This one gets close: https://dasher.wustl.edu/bio5357/software/chimerax/tutorial.pdf > > THANK YOU for answering on a Sunday!! > Anne-Frances > >

3 3

abbreviation for transparentbackground please
by Anne-Frances Miller 12 Jan '25

12 Jan '25

Dear Sir or Madam, Re. ChimeraX 1.7: the image save option ’transparent background true’ is very long, and typo-prone. Is there an abbreviation or short form please? Thank you - • - • - • - • - • - • - • - • - A.-F. Miller, Ph. D. (she/elle/sie) University Research Professor Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin

5 8

Problem upgrading to the latest version 1.9
by svle＠tiscali.it 09 Jan '25

09 Jan '25

Hi, surely for my errors in uninstalling the previous version , I'm receiving the following: $ sudo apt remove --purge ucsf-chimerax Reading package lists... Done Building dependency tree... Done Reading state information... Done The following packages were automatically installed and are no longer required: libgdk-pixbuf-xlib-2.0-0 libgdk-pixbuf2.0-0 libosmesa6 libxcb-cursor0 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: ucsf-chimerax* 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 0 B of additional disk space will be used. Do you want to continue? [Y/n] (Reading database ... 524167 files and directories currently installed.) Removing ucsf-chimerax (1.9ubuntu24.04) ... Deregister desktop menu and associated mime types /var/lib/dpkg/info/ucsf-chimerax.prerm: 4: chimerax: not found dpkg: error processing package ucsf-chimerax (--remove): installed ucsf-chimerax package pre-removal script subprocess returned error exit status 127 dpkg: too many errors, stopping Errors were encountered while processing: ucsf-chimerax Processing was halted because there were too many errors. E: Sub-process /usr/bin/dpkg returned an error code (1) $ dpkg --get-selections | grep ucsf ucsf-chimerax install $ chimerax chimerax: command not found Any suggestions to recover? Thanks. Saverio

2 1

Saving restraints
by Dyda, Frederick (NIH/NIDDK) [E] 07 Jan '25

07 Jan '25

I was wondering if there is a way to save restraints that one set up for a particular structure. For instance if I set up a bunch of "Simple Distance Restraints" in Isolde, to restrain a metal coordination environment, can I save these so I can reuse them for another .pdb file (assuming residue numbering is the same). Thanks. Happy New Year! Fred ******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 NIDDK Bldg. 5. Room 338 e-mail: Fred.Dyda(a)nih.gov Bethesda, MD 20892-0560 URGENT message: 2022476710(a)msg.fi.google.com Google map: 39.001168, -77.102048 http://www-mslmb.niddk.nih.gov/dyda/dydalab.html *******************************************************************************

2 2

Assistance/guidance with ChimeraX
by Mahesh Chandrasekharan 03 Jan '25

03 Jan '25

Hi: First up, thank you and your team for all your efforts in creating and maintaining Chimera and ChimeraX. They are an awesome tool/package! It would be very helpful if you could please assist me with the two questions below. 1) I have a PDB downloaded from Alphafold. I would like to ‘drag out’ or reposition regions in order to enable their better visualization for a figure that I need for a grant. How can I select and reposition specific regions of a protein structure in ChimeraX? 2) The protein of my interest is a homodimer. I would like to open two copies of the relevant PDB file and manipulate them as two separate proteins. I have made a duplicate and relabeled the PDB file. However, when I open it ChimeraX along with the original, the two files seem linked, and I am unable to work on them separately. Is there a way to open two copies of the same PDB file to ‘recreate’ a homodimer? Thank you, Best, Mahesh Mahesh B. Chandrasekharan, PhD Assistant Professor of Radiation Oncology Investigator, Huntsman Cancer Institute Adjunct Assistant Professor of Hematology & Hematological Malignancies University of Utah School of Medicine 2000 Circle of Hope Room 3715 Huntsman Cancer Institute Salt Lake City, UT 84112-5540 Phone: 801-213-4220 Administrative Assistant: Coreen Rankin (801-585-3599) Lab site: https://uofuhealth.utah.edu/huntsman/labs/chandrasekharan

2 1

Getting average of PAE values for a given region / interaction
by David S. Fay 02 Jan '25

02 Jan '25

Greetings and Happy New Year to All! My question is about broadly protein-protein interactions (PPIs. Last year several manuscripts came out proposing new metrics for assessing PPIs. This was in logical response to the growing understanding that ipTM (alone) is a fairly flawed metric, particularly for detecting interactions that involve a small number/fraction of the total residues. For those interested, I’ve pasted links to three such papers below (Coincidentally one is from a former roommate's lab, which I didn’t notice until recently!). Some may be easier to use than others (have GUIs). Tom Goddard and I emailed back and forth a bit about the relative merits of some of these metrics - nothing is perfect obviously (thank you again Tom). With respect to ChimeraX, I was wondering if there was a way to extract average PAE values after employing a cutoff. For example, "alphafold contacts /A distance 5 maxPae 5” will tell me that are "54 residue or atom pairs within distance 5 with pae <= 5”. But what if I want to know the average of those 54? Along those lines, for some PPIs there may be several spatially separated interfaces, with each one contributing to the total number. Is there an easy way to obtain the average and other metrics for each one? Some of this information I could probably find in my clunky (borderline boomer) way, by filtering, adding, and averaging values from the pairwise data (perhaps made easier by Predictome). Lastly, drawing rectangles on the PAE plot does a great job of giving coordinates and the average PAE, but it doesn’t give the range or other potentially useful data, such as the number of PAE<5 values etc. I guess I’m thinking that it could be very useful to be able to get metrics for a prescribed region of the PAE plot simply by drawing the rectangle. (And maybe there is but I missed it.) Those are my questions and thoughts. But I also wanted to express my gratitude for the ChimeraX software, and even more, the people working at ChimeraX who are always exceptionally responsive and helpful. David https://www.biorxiv.org/content/10.1101/2024.02.19.580970v1 https://www.biorxiv.org/content/10.1101/2024.10.23.619601v1 https://www.biorxiv.org/content/10.1101/2024.04.09.588596v1 David S. Fay Ph.D. Professor, Department of Molecular Biology Associate Director, National Institutes of Health Wyoming INBRE University of Wyoming email: davidfay(a)uwyo.edu

2 1

get help with changing the cartoons ribbon to ball sticks
by Nhi Hoang 02 Jan '25

02 Jan '25

Hi. I am a sophomore at Le Quy Don High School in Danang City, Vietnam. I am using ChimeraX to display a model for my little project, and I have found a small trigger that I want to get help with. My problem is I cannot change the cartoon of selected residues from ribbons to ball sticks, after I have preset the model with cartoon ribbons. I wonder if this problem is due to the application and its limits or because of my device. I have attached an image presenting the coding and the model for a clear description of my problem. If possible, I am really willing to receive some advice from you in tackling this problem. Thank you very much. Best, Nhi Hoang. [image: image.png]

2 2

Vector in ChimeraX
by Vitali James 30 Dec '24

30 Dec '24

Dear ChimeraX, Can you please help me to connect two pseudo-atoms by vector in ChimeraX. In the attached image (chimera.png), it was smoothly done in the past, but now the same file looks like a dotted line in chimeraX( e.g vector.PNG). Is it possible to control the color and style of this dotted vector line? best regards J. Vitali

2 1

Quest 2 Support?
by Blaine Hewitt 27 Dec '24

27 Dec '24

Hello, my name is Blaine Hewitt. Now I know that you have stated previously that you have no intention of bringing support to the Oculus Quest. Which is completely understandable since I know that not only would you have to develop around a completely new Operating System but another CPU architecture and much much more I assume. But with the soon release of the Oculus Quest 2 and it's new XR 2 chip-set makes a pretty good argument for it. As this would allow for much easier use in education (as is what I am attempting to do with it). I think it will be even easier now to push updates with SideQuest <https://sidequestvr.com/> being relatively simple to setup. I know that another (Naome <https://blog.matryx.ai/nanome-on-quest-public-beta-is-now-available-b546321…>) program is already available on the platform. But I do like your program a lot more since it is able to be used for free unlike Nanome Pricing <https://nanome.ai/pricing/> which is... as to say unappealing to public schools (such as mine). I was was also thinking (sorry if I am becoming annoying at this point) that if you do make a version of the Quest that you could make that GitHub branch available to the public. As for example while I may not be great at understanding complex protein structures I can help to make the whole experience more user friendly. Anyways if you read this far thank you for taking time from your day to read this. If you want to know who I am, my name is Blaine I am in my senior year of High School (Waynecsd <https://wh.waynecsd.org/>). I have to do a project by the end of the year where I have to present an area of study I want to pursue and I decided to research the effects of VR on the human's ability to learn and retain information. Budget..... None

4 3

Unable to show interactions between bases and protein
by ADINDA 27 Dec '24

27 Dec '24

Dear Chimerax team, Hi, I am trying to find the interactions between my RNA and protein but have been unable to do so. I've been using the "contacts" function but it's not been working as expected. The command line that I gave was: contacts #1.2 restrict #1.1 makePseudobonds true reveal true log true where #1.2 is my RNA and #1.1 is my protein. Even when I switch the positions of #1.2 and #1.1, it still doesn't work (0 contacts shown). Do you have any tips on how I can rectify this? Happy holidays! Best regards, Adinda

2 1

How probe radius should affect exposed surface area?
by Alon BenDavid 25 Dec '24

25 Dec '24

Hi, I am trying to measure the exposed surface area of lysine residues in DNaseI (4AWN). I am using the "measure sasa" command. To my surprise, when I am increasing the probe radius (1.4 A, 5 A, 10 A etc.) I receive larger exposed surface area. Is that OK? Many thanks, Alon

2 1

cartoon style setting
by junjie han 23 Dec '24

23 Dec '24

Hi, May I ask how I can set the cartoon thick for a specific region of a structure in ChimeraX? For instance, the command "cartoon style #1/A:10-20 thick" plays an effect on the whole #1 molecule, not only affecting the specific region #1/A:10-20. Please let me know what the appropriate command is by any chance. Thanks, Junjie

2 3

"straightening" or stretching disordered residues from alphafold models
by Daniel Elnatan 19 Dec '24

19 Dec '24

Hi folks, I’ve been playing around with AlphaFold to get protein structures and visualizing them in ChimeraX. For some proteins with a lots of disordered regions (e.g. between non-interacting, well-folded domains), the ‘noodles’ end up being a visual clutter. So I wrote a custom python function to be used in ChimeraX that would ‘straighten’ or stretch selected residues (typically the disordered or low pLDDT regions) by simply assigning torsion angles for a more ‘straight’ structure. I do this via the `Residue.set_phi()` and `Residue.set_psi()` methods. Here’s a link to my Python script: https://github.com/delnatan/colabfold_chunker_utils/blob/65f2419425de300df5… The command is run simply with `straighten #1:13-20`. Now when there are multiple chains within the same model, altering the torsion angles may actually move the relative positioning between the chains. Is there an easy way to avoid this? perhaps by passing an extra argument as ‘reference’ so one can place the structure back to its original coordinate for the reference residues. I’m not too familiar with the programming API just yet, but what is the correct way to do this? Maybe that the reference coordinates can be saved before assigning the torsion angles, and a transformation matrix can be computed only for the reference region between the original and moved structure. The altered chain can then be moved back by applying this transformation matrix? Thanks! -Daniel

3 6

Help with ChimeraX modeling
by Christman, Nick 18 Dec '24

18 Dec '24

Hello, I am a graduate student at Indiana University, and I am trying to use ChimeraX to visualize positively charged surface accessible residues on some protein models. I've been trying to find the right combination of commands to get this to work but haven't been successful. I know how to calculate surface accessible residues, how to color the surface accessibility of residues within a selection on my model, and even how to calculate hydrophobicity of residues (related to charge), but I cannot figure out how to model the charge of surface exposed residues. Could you please point me in the right direction so I can get the models that I would like? Thanks! Nick Christman (He/Him) Dalia Lab Indiana University

2 1

poc file of castp not support
by Prem Dorjee Tamang 17 Dec '24

17 Dec '24

sir/madam this chimer_x version 1.8 and 1.9 both the tools not support the poc file just look in thes matter

2 1

initial dark mode support
by Greg Couch 16 Dec '24

16 Dec '24

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

2 3

Re: [chimerax-announce] ChimeraX version 1.9 has been released
by Elaine Meng 16 Dec '24

16 Dec '24

Hi Dietmar, Thanks for your comments. Unless you refer to data that must be kept private, it is best to send questions and suggestions to the chimerax-users mailing list (CC'd here) rather than to me or any other individual team member. That way the most relevent people can see/answer your question and other users can weigh in if they also wish for the same thing. You could use the Help menu to open the ChimeraX User Guide that is included with your download instead of googling the web. You can also use the context menu in each tool (or its Help button, if it has one), to open the ChimeraX manual page for that tool, and the "help" command to show the manual page for each ChimeraX command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/help.html> Unfortunately the ChimeraX Help menu does not have a search feature, although that is probably on our list of requests already. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 13, 2024, at 12:29 PM, Dietmar Funck <dietmar.funck(a)uni-konstanz.de> wrote: > > Dear Elaine, dear ChimeraX developer Team, > > thanks for the release of ChimeraX 1.9. I am confident that it will be as great or even better than 1.8 :-) > > I have two requests/suggestions how your could improve ChimeraX further: > > a) the metal coordination function seems to be still missing in ChimeraX (or it is so well hidden that I wasn’t able to find it). > > b) You could teach Google that there is a difference between Chimera and ChimeraX. Each time, I try to find solutions to problems with ChimeraX, I get results from the user guide of Chimera, which usually don’t solve the problem. > > All the best, > > Dietma > > Dietmar Funck > Biopolymer Chemistry > Chemistry Department > University of Konstanz

3 2

embed ChimeraX into web pages
by Marius Mihasan 12 Dec '24

12 Dec '24

Hi I have been using ChimeraX for some time to generate .stl files and print various molecules and molecular scenes. I planning/working on making the pdb to stl file conversion semi-automatic and more user friendly by offering the users some predefined 3D-printable renderings of the molecule of their choice as well as some simple push-buttons that would allow them to do some very simple customisation in the renderings. Everything needs to be packaged in a simple to acces web-page that can be used by educators and students . In a way similar to how NIHPresets work, but in a webpage. Or how NIH 3D QuickSubmit works, but more interactive. Is there a way to embed ChimeraX into web pages as it can be done with, for example, with JSmol (Jmol)? If yes, could someone please point me in the right direction? Thanks --------- Marius Mihasan, PhD. Habil. Professor, BioActive Research Group Biochemistry and Molecular Biology Laboratory, Faculty of Biology Alexandru Ioan Cuza University of Iasi Room B228, Carol I Blvd, no 20A, Iasi, Romania, 700506 Tel: +40(0)232202434 Fax: +40(0)232201472 http://cercetare.bio.uaic.ro/cadre/pagini-personale/marius.mihasan/index.ht… Associate Professor Darie Biochemistry & Proteomics Group Department of Chemistry & Biomolecular Science Clarkson University Potsdam, NY 13699-5810, USA mmihasan(a)clarkson.edu

3 3

Chimerax install error
by 王康瑞 11 Dec '24

11 Dec '24

Greetings! I'm a student from Tsinghua university, thank you for your contribution. I encountered a error when I installing ChimeraX, and I pasted it in the attach files below. I was able to launch chimerax with option"--nogui", and "--help" option seems run successfully too, but the ui didnt work. Thank you! Best wishes, Kyrie.

3 3

Question about translating/rotating individual chains in a model
by John Watters 11 Dec '24

11 Dec '24

Hi all, I was wondering if anyone had any suggestions on how to rotate and translate a DNA-bound protein model one base pair at a time (essentially walking the protein down the double helix) so I can compare its interactions with another protein. My plan was to define a vector between the center of mass of each nucleotide pair to then move the DNA-bound protein one average pitch length using the move command and rotation using the turn command one nucleotide at a time. When I try to save these new models using "save pdf_filepath.pdb models #3 relModel #1" the DNA-bound protein is still in the original position - do I need to modify the save command or move the DNA-bound protein using different commands? Thanks for any help you can provide! Best, John

2 1

chimeraX 1.9rc202412100000 and copy/paste from the log panel not possible
by Vincent CHAPTAL 11 Dec '24

11 Dec '24

Hi, after upgrading to 1.9rc202412100000, I can't copy/paste a command from the log panel, typically the "view matrix" for the orientation. I tried it on 1.7 and it works with the 2 chimeraX sessions working at the same time. (haven't tried it on 1.8). Is there something specific I'm missing? I'm using macOS 14.6.1 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/

2 2

Z-flip option for fitmap?
by Oliver Clarke 11 Dec '24

11 Dec '24

Hi, I frequently use fitmap with global search to quickly fit an initial model to low resolution EM maps at early stages of data processing. At low resolution, it is often not immediately obvious which hand of the map is correct, so I will fit to both the original map and one that has been Z-flipped. Would it be possible to add an option to do this automatically, similar to how the "resolution" flag fits a molmap of the model at the specified resolution to the map? Cheers Oli

3 5

display pseudobonds between atoms as solid line
by Vincent CHAPTAL 11 Dec '24

11 Dec '24

Hi, I've been playing a lot with the commands but I can't seem to get it right. I'd like to display a line between 2 atoms in a model. I tried: pbond #2.1:940@O #2.1:472@O reveal true color blue dashes 1 (and variations around it) but I got an error that pbond or pseudobond are unknown commands. I also played around with distance: distance #2.1:940@O #2.1:472@O hide #4.1 color #4 blue distance style #4 dashes 0 but the distance does not appear on my screen. Could you help me work this out? 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/

3 4

Connecting ChimeraX to Cytoscape via your structureVizX.zip file
by Jean-François Bureau 11 Dec '24

11 Dec '24

Hi, I already use Chimera to cytoscape and I would like to add chimeraX. I downloaded your structureViZ.zip file and open it but I did not find what to do next. Thank you for your help Regards JF Bureau Institut Pasteur Paris, France

2 1

Mac with nogui to run batch cmd
by aponysbc＠gmail.com 10 Dec '24

10 Dec '24

Hi, I'm trying to generate images in batch with chimerax from terminal on mac m2. When I run "chimerax --nogui --exit --cmd" I get the error: raise LimitationError("Unable to save images because OpenGL rendering is not available") chimerax.core.errors.LimitationError: Unable to save images because OpenGL rendering is not available ChimeraX command "graphics driver" gives: OpenGL version: 4.1 Metal -88.1 OpenGL renderer: Apple M2 OpenGL vendor: Apple Is there any way around this? I saw another post about this from 2020 that the nogui option only works on linux with offscreen. Is there any way to save images in batch from terminal? Thanks, Aaron

2 2

Intra-chain contacts
by Rosaleen Calvert 10 Dec '24

10 Dec '24

Hi How do I get a text file of contacts A-B (NOT A-A or B-B). I have tried Show atoms Select Contacts Chain A on left. Chain B on right Uncheck intermodel Check file. Please help. Thanks. Rosy

2 4

Error during flipping to change the handedness of the cryo-EM map
by Shardul Dhole 10 Dec '24

10 Dec '24

Hi, I was trying to change the map's handedness while trying to fit two maps in ChimeraX. However, when I use the command vop flip #3 (3 is my model number), it gives an error: *"**Expected a density maps specifier or a keyword." * How to overcome this? Thank You. -- Regards, Shardul Dhole.

2 1

ChimeraX 1.8 release
by Elaine Meng 10 Dec '24

10 Dec '24

UCSF ChimeraX version 1.8 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html Updates since version 1.7 (Dec 2023) include: - show worm depictions of attribute values (B-factor, conservation, etc.) using Render by Attribute tool or "cartoon byattribute" command - show attribute values with atomic radii using Render by Attribute or "size byattribute" - Select by Attribute graphical interface - Join Models generalized to any covalent bond (not just peptide) - show multiple alternate locations simultaneously with "altlocs show" - "pbond" command to create arbitrary pseudobonds - "measure contactarea" to report the area of one surface within a cutoff distance of another - Segmentations tool for interactive manual segmentation in 2D slice views, 3D (desktop), or 3D (VR) can be applied to any volume data, not just medical images; several fixes and ergonomic improvements including icons to assign/deassign mouse and VR hand-controller modes with a single click - set up and analyze batch AlphaFold predictions to search for protein-protein interactions (commands for advanced users who can run ColabFold directly on Linux) support for: - reading predicted aligned error (PAE) data from AlphaFold 3 - reading docking results from MOE - fetching atomic structures and maps from PDB-REDO - fetching/display of PDB NMR-STAR restraints For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

2 13

ChimeraX with Modeller
by Matt Goff 09 Dec '24

09 Dec '24

Hi Guys, I am trying to use ChimeraX with Modeller to fill in a few small gaps in my PDB file. However, when I run modeller from ChimeraX I get the following error: dyld[77819]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python Referenced from: <498CB722-A7BC-378D-A38D-3A690F9D635B> /Library/modeller-10.6/bin/mod10.6_mac10v4 Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file) Exception in thread Thread-10 (threaded_run): Traceback (most recent call last): File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/modeller/common.py", line 708, in threaded_run _ = subprocess.run(cmd, capture_output=True, text=True, check=True, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py", line 571, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/Library/modeller-10.6/bin/mod10.6_mac10v4', '/var/folders/wn/dw9ws1756cjfsv3p6m3lphmc0000gn/T/tmpj5w_luqj/ModellerModelling.py']' died with <Signals.SIGABRT: 6>. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038, in _bootstrap_inner self.run() File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975, in run self._target(*self._args, **self._kwargs) File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/modeller/common.py", line 720, in threaded_run raise UserError("Modeller execution failed; output and errors in log") chimerax.core.errors.UserError: Modeller execution failed; output and errors in log It seems that the python2.7 is the issue, but I’m not sure which file to edit to point it to a new version (I’m on python 3.12). I’ve also tried this with ChimeraX 1.9 and 1.8 with the same error. Can you point me in the right direction? Thanks! Matt Goff

3 3

Installing ChimeraX in a Apptainer container
by tluchko 08 Dec '24

08 Dec '24

Hello, I am trying to install ChimeraX in an apptainer (singularity) container. I am able to load molecules but running into two issues. - I get a lot of python tracebacks (see below). I have also installed ChimeraX directly on the same machine from the RPM and do not see these error messages. - Rendering is very slow, so I don't think it is using the graphics card. The direct installation is similarly slow, but I have installed VMD on the same system and I can tell that it is using the graphics card, both from the log and the speed. Please let me know if you have any suggestions to address either of these issues. This is the command that I am using to launch ChimeraX apptainer exec --bind /tmp/.X11-unix,/storage/storage1 --env DISPLAY=$DISPLAY --nv chimerax-rocky9.sif chimerax This is the definition file for the container. BootStrap: docker From: rockylinux/rockylinux:9.4 %labels Maintainer Tyler Luchko Version 1.0 %help This is a Rocky Linux 9 container for ChimeraX 1.8 %setup # These are only required if running on the HPC. #mkdir -p ${APPTAINER_ROOTFS}/tmp mkdir -p ${APPTAINER_ROOTFS}/scratch %post echo "Installing packages into the Rocky Linux 9 container" dnf -y install yum-utils dnf -y config-manager --set-enabled crb dnf -y install epel-release dnf -y install mesa-dri-drivers glx-utils dnf -y install /tmp/ucsf-chimerax-1.8-1.el9.x86_64.rpm dnf clean all %environment export PATH=/usr/bin:/usr/sbin:/bin:/sbin export SHELL=/bin/bash export LANG=en_US.UTF-8 Sample error output is below. Thank you, Tyler NOTE: available bundle cache has not been initialized yet NOTE: Traceback (most recent call last): File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1286, in start_tool return cls._get_func(api, "start_tool")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/log/__init__.py", line 50, in start_tool return cmd.get_singleton(session, create=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/log/cmd.py", line 30, in get_singleton return tools.get_singleton(session, Log, 'Log', create=create) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/tools.py", line 216, in get_singleton tinst = tool_class(session, tool_name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/log/tool.py", line 161, in __init__ from chimerax.ui.widgets import ChimeraXHtmlView ImportError: cannot import name 'ChimeraXHtmlView' from 'chimerax.ui.widgets' (/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/ui/widgets/__init__.py) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/tools.py", line 418, in start_tools bi.start_tool(session, tool_name) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 578, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Log in bundle ChimeraX-Log: cannot import name 'ChimeraXHtmlView' from 'chimerax.ui.widgets' (/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/ui/widgets/__init__.py) BUG: Tool "Log" failed to start: chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Log in bundle ChimeraX-Log: cannot import name 'ChimeraXHtmlView' from 'chimerax.ui.widgets' (/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/ui/widgets/__init__.py) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 578, in start_tool raise ToolshedError( _See log for complete Python traceback._ NOTE: UCSF ChimeraX version: 1.8 (2024-06-10) NOTE: © 2016-2024 Regents of the University of California. All rights reserved. NOTE: [How to cite UCSF ChimeraX](cxcmd:help help:credits.html) NOTE: Traceback (most recent call last): File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/bug_reporter/crash_report.py", line 138, in _delayed_register_log_recorder _register_log_recorder(session) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/bug_reporter/crash_report.py", line 172, in _register_log_recorder log.record_to_file(log_file) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/log/tool.py", line 410, in record_to_file self._log_to_file(self.page_source) ^^^^^^^^^^^^^^^^ AttributeError: 'Log' object has no attribute 'page_source' BUG: Error processing trigger "new frame": AttributeError: 'Log' object has no attribute 'page_source' File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/log/tool.py", line 410, in record_to_file self._log_to_file(self.page_source) ^^^^^^^^^^^^^^^^ _See log for complete Python traceback._ Sent with [Proton Mail](https://proton.me/mail/home) secure email.

3 3

Changing range for electrostatic potential coloring
by Eric Martz 07 Dec '24

07 Dec '24

I want to have less white and more color on an electrostatic potential map. I suspect this is done by reducing the range, but I can't find how to do this. I start with open 1bl8 fromDatabase pdb format mmcif select protein coulombic sel ui tool show "Surface Color" Then I have this dialog, where I have changed -10 ... +10 to -5 ... +5 When I click the Color button, I get "No map chosen for coloring", but the "using map" menu has no options. ??? Also I would like to re-color the surfaces for all 4 chains, not one at a time, but the "Color surface" menu seems to have 4 separate chain surfaces, but no option for all 4 at once. I will appreciate guidance! Thanks, -Erichttp://martz.molviz.org

3 5

Coloring charged amino acids
by Eric Martz 06 Dec '24

06 Dec '24

Consider this: open 1pgb fromDatabase pdb format mmcifstyle sphereshow atoms 1. What is the command to hide all water? 2. How do I color charged amino acids, leaving uncharged one a neutral color (such as white)? I was hoping there was a menu item or command that would do something similar to this: color all whitecolor :lys,arg bluecolor :glu,asp redcolor :his lightblue without having to type all those commands. FirstGlance in Jmol and iCn3D have "one click" ways to do this, but I don't see one in ChimeraX or MolStar. Thanks, -Eric

2 2

Deleting hydrogen
by Eric Martz 05 Dec '24

05 Dec '24

I have studied the help delete.html but have been unable to guess the command syntax to delete all hydrogen atoms. Unfortunately, that help page has no examples. Please tell me the command. Thanks, -Eric

2 2

Centering?
by Eric Martz 05 Dec '24

05 Dec '24

I have spent over an hour failing to come up with the command that will move the molecule (and its center of rotation) to the center of the viewport. I see that "cofr all" places the center of rotation in the center of mass of what is loaded. But I have been unable to find the command to move it to the center of the viewport. I realize that I can drag it to approximate center of viewport with right-drag, but I'd like a command to do this. For example, load anything, drag it off center, then what is the command to move it back? Thanks, -Eric

2 1

duplicate the map view
by Vitali James 04 Dec '24

04 Dec '24

Dear Chimera users I have to make a slice of a map on the selected atom. Is it possible to duplicate this map view? in chimeraX James

3 5

Adding/editing chains' description
by André Graça 04 Dec '24

04 Dec '24

Hi everyone! I am missing a way to add/edit chain descriptions in ChimeraX. Is it possible? If not, would this be a reasonable request to plan for a future release? Wishing a nice day to whoever reads this message =) André ________________________________ From: chimerax-users-request(a)cgl.ucsf.edu <chimerax-users-request(a)cgl.ucsf.edu> Sent: Monday, December 2, 2024 10:52 PM To: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> Subject: ChimeraX-users Digest, Vol 96, Issue 1 Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..." Today's Topics: 1. Re: [Chimera-users] Movie from pdb file with 30 models of a conformational change. (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 2 Dec 2024 13:52:23 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: [chimerax-users] Re: [Chimera-users] Movie from pdb file with 30 models of a conformational change. To: Evan Kantrowitz <kantrow(a)bc.edu> Cc: Eric Pettersen via Chimera-users <chimera-users(a)cgl.ucsf.edu>, chimerax-users <chimerax-users(a)cgl.ucsf.edu> Message-ID: <0368B293-FF58-4F72-97C0-51DF75D23035(a)cgl.ucsf.edu> Content-Type: multipart/mixed; boundary="Apple-Mail=_5630A7C6-3B74-4E39-A0F1-3F2D7DF8DDB0" Hi Evan, Your image looks nice! From your screenshot I can see you are using ChimeraX (not Chimera) so I will answer for ChimeraX ( there is a different email address for ChimeraX questions, chimerax-users(a)cgl.ucsf.edu CC'd here). To "play" the conformational change there are a couple of options: (1) if the models are already open as a set of multiple models as shown in your screenshot, you can use command: mseries slider #1 ...which will open a slider interface that you can click play, record movie, etc. Or, you can play through the series with the "mseries" command. <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf…<https://rbvi.ucsf.edu/chimerax/docs/user/commands/mseries.html>> (2) Or, you can use the "coordsets true" option of the "open" command when opening the file, <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf…<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#coordsets>> which means to interpret the file as a single trajectory instead of a series of models. That will automatically show a slider interface. Example: open blahblah.pdb coordset true If you want to use the file browser to find your PDB file, you can use command open browse coordsets true ...and it will open the file browser for you to find and choose the file. If you have a trajectory, you can also play through it with the separate "coordset" command. <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf…<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>> More info, general explanation of model series vs. trajectories <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf…<https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html>> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 2, 2024, at 1:31 PM, Evan Kantrowitz via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > > Can someone give me help with a, I think, simple issue. I have a single pdb file containing 30 MODELS > These 30 models correspond to a conformational change. Here is a portion of the Models list-------------- next part -------------- A message part incompatible with plain text digests has been removed ... Name: PastedGraphic-1.png Type: image/png Size: 44782 bytes Desc: not available -------------- next part -------------- > > When I read it in,I see all 30 models showing in the view. > What I want to do is make a movie showing these 30 MODELS one after the other. I have tried coordset and coordset slider but have not got it to work. > > Thanks > > Evan > > PS. This is what the image looks like with the 30 frames.It was generated from the A chain of pdb files 2e2n and 2e2q using the website ViewMotions (viewmotions.bc.edu).-------------- next part -------------- A message part incompatible with plain text digests has been removed ... Name: PastedGraphic-2.png Type: image/png Size: 113501 bytes Desc: not available -------------- next part -------------- > > > ----------------------------------------------------------------------------- > Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu > Emeritus Professor of Chemistry Cell: 617-775-9915 > Boston College www2.bc.edu/evan-kantrowitz ----------------------------------------------------------------------------- ------------------------------ Subject: Digest Footer _______________________________________________ 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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.…<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/> ------------------------------ End of ChimeraX-users Digest, Vol 96, Issue 1 *********************************************

2 3

ChimeraX Download
by Wagner, Elina Lynge 04 Dec '24

04 Dec '24

Hello, I have been trying to download ChimeraX but get the error message that x64 is needed. I currently have a Microsoft Surface Laptop 7th Edition. The processor is Snapdragon(R) X 10-core and the system type is 64-bit operating system, ARM-based processor. Even though I have the 64-bit operating system, will I be unable to download the program due to having an ARM processor? If this is correct, will there be a version of ChimeraX that will be able to run on new windows 11 computers (surface pro 11 and surface laptop 7)? Have a great day, Elina Lynge Wagner The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

2 1

Adding a label to MRC map file header
by Tom Goddard 03 Dec '24

03 Dec '24

Hi Raman, I'm not sure where in the MRC binary file this "EXPDATA EM" is suppose to go, maybe a "label" field. As you can see from the MRC file spec it has space for 10 labels in bytes 225-1024 of the header https://www.ccpem.ac.uk/mrc_format/mrc2014.php ChimeraX has no options to insert specified text into those labels, but you could edit the ChimeraX Python code that writes the MRC file to add a label. The file is called writemrc.py and is in your ChimeraX distribution, on Mac it is here ChimeraX.app/Contents/lib/python3.11/site-packages/chimerax/map_data/mrc/writemrc.py Here's what this code looks like in the ChimeraX Github repository https://github.com/RBVI/ChimeraX/blob/00c7ef34fdf8e3f9675cf892f346adbecbfe6… It has some lines that put a ChimeraX version and time stamp into the MRC file ver_stamp = 'ChimeraX %s %s' % (version, asctime()) labels = [ver_stamp[:80]] You could add a line after that labels.append('EXPDATA EM') to add a label with that string. then restart ChimeraX and save a map (e.g. command "save mymap.mrc"). Another approach would be to open the mrc file in a binary editor and carefully modify some of the bytes from 225-1024 to add your label. Of course all this assumes that EXPDATA EM is supposed to go in a label and not for instance the EXTRA bytes part of the header. It seems absurd that you have software that won't work without a special label in the file. Tom > On Dec 3, 2024, at 4:47 PM, Raman, C.S. <craman(a)rx.umaryland.edu> wrote: > > Hi Tom, > > Is there an easy way to insert into the header of an MRC file the descriptor "EXPDATA EM" as done by the PDB? I need to do this to run a validation program but don't quite know how to go about it. > > Any help would be greatly appreciated. > -raman

1 0

Re: [Chimera-users] Movie from pdb file with 30 models of a conformational change.
by Elaine Meng 02 Dec '24

02 Dec '24

Hi Evan, Your image looks nice! From your screenshot I can see you are using ChimeraX (not Chimera) so I will answer for ChimeraX ( there is a different email address for ChimeraX questions, chimerax-users(a)cgl.ucsf.edu CC'd here). To "play" the conformational change there are a couple of options: (1) if the models are already open as a set of multiple models as shown in your screenshot, you can use command: mseries slider #1 ...which will open a slider interface that you can click play, record movie, etc. Or, you can play through the series with the "mseries" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/mseries.html> (2) Or, you can use the "coordsets true" option of the "open" command when opening the file, <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#coordsets> which means to interpret the file as a single trajectory instead of a series of models. That will automatically show a slider interface. Example: open blahblah.pdb coordset true If you want to use the file browser to find your PDB file, you can use command open browse coordsets true ...and it will open the file browser for you to find and choose the file. If you have a trajectory, you can also play through it with the separate "coordset" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> More info, general explanation of model series vs. trajectories <https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 2, 2024, at 1:31 PM, Evan Kantrowitz via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > > Can someone give me help with a, I think, simple issue. I have a single pdb file containing 30 MODELS > These 30 models correspond to a conformational change. Here is a portion of the Models list > > When I read it in,I see all 30 models showing in the view. > What I want to do is make a movie showing these 30 MODELS one after the other. I have tried coordset and coordset slider but have not got it to work. > > Thanks > > Evan > > PS. This is what the image looks like with the 30 frames.It was generated from the A chain of pdb files 2e2n and 2e2q using the website ViewMotions (viewmotions.bc.edu) > > > ----------------------------------------------------------------------------- > Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu > Emeritus Professor of Chemistry Cell: 617-775-9915 > Boston College www2.bc.edu/evan-kantrowitz -----------------------------------------------------------------------------

1 0

ChimeraX-1.8 functionality regarding the match command
by Nicholas Ferraro 02 Dec '24

02 Dec '24

Good morning, My name is Nicholas Ferraro. I am a graduate student at the City College of New York. I am currently using ChimeraX-1.8 to visualize multiple PDBs of the hexameric helicase I am working with. We have labeled each protomer of the hexamer A-F. I understand the software allows for matching structures either by best-aligning pair of chains, a specific reference structure to the best-aligning chain, and specific chains in a reference structure with specific chains in the matching chain. I have six PDBs. What I want to do is align all chains with respect to their chain ID and specific sequence. Can you advise on how to accomplish this in chimera-1.8? Thank you for you assistance. Please let me know if you need more details. Best, Nicholas Ferraro

2 1

Stepping through model in secondary structure element steps (ISOLDE)
by Vorländer,Matthias Kopano 28 Nov '24

28 Nov '24

Dear all, I seem to remember that it was possible to step through a model in Isolde one secondary structure element at a time, however I don't find that option anymore. Is this possible at all? I prefer this to the isolde step option that goes through the model one residue at a time. Many thanks in advance, Matthias Sent from Outlook for Android<https://aka.ms/AAb9ysg> --- Matthias Kopano Vorländer Postdoc matthias.vorlaender(a)imp.ac.at<mailto:matthias.vorlaender@imp.ac.at> Plaschka Lab IMP - Research Institute of Molecular Pathology - imp.ac.at<https://imp.ac.at/> Part of Vienna BioCenter. www.viennabiocenter.org<https://www.viennabiocenter.org>

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Re: IMOD Segmentation to ChimeraX (.mod to .cmm Conversion)
by Tom Goddard 27 Nov '24

27 Nov '24

Glad you got it to work. Tom > On Nov 27, 2024, at 3:30 PM, LENKA MILOJEVIC <lenka11(a)g.ucla.edu> wrote: > > Dear Dr. Goddard, > > Thank you so much! That worked! I thought I’d have to produce a .cmm file or mask the map using the volume tool and the .mod file as a surface. > > I really appreciate your swift responses! This was incredibly helpful. > > Have a great rest of your day! > > Sincerely, > Lenka > > On Wed, 27 Nov 2024 at 15:26, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Lenka, >> >> Seems like you got what you wanted "I was wondering if there's any way that I could convert the .mod file into a .cmm file because my goal is to segment a map in ChimeraX using the Color Zone tool, according to the contours from IMOD." Your image shows the traced curves as connected markers (fake atoms connected by bonds). To color the nearby density you would then use the Color Zone tool, menu Tools / Volume Data / Color Zone and it has a Split Map button that would let you make a new map that includes just the colored part near your curves. The equivalent ChimeraX command is "color zone" >> >> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#zone >> >> If the command syntax is confusing just use the graphical Color Zone tool and it will log the equivalent command to the Log panel and you will have a better idea of how to type a command if you want to use some of the fancier options (like bondPointSpacing) that the graphical tool does not offer. >> >> Tom >> >> >>> On Nov 27, 2024, at 2:46 PM, LENKA MILOJEVIC via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> In the event that I want to mask map #3 using the .mod file in #1 , which command exactly do I run? I'm attaching a screenshot showing my current session. >>> <image.png> >>> >>> >>> On Wed, Nov 27, 2024 at 2:42 PM LENKA MILOJEVIC <lenka11(a)g.ucla.edu <mailto:lenka11@g.ucla.edu>> wrote: >>>> Hi Elaine, >>>> >>>> If I don't input contours true, nothing shows up on my screen. It just states it read it. >>>> open <> C:/Users/lenkamilojevic/Box/HSV-1/Front/HSV1_9_overcoils.mod >>>> Read IMOD model C:/Users/lenkamilojevic/Box/HSV-1/Front/HSV1_9_overcoils.mod, pixel size 0.568 >>>> >>>> Sorry for the trouble. I really appreciate your help. >>>> >>>> Best, >>>> Lenka >>>> >>>> On Wed, Nov 27, 2024 at 2:09 PM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >>>>> Hi Lenka, >>>>> Contours true is to make it into markers and links (fake atoms and bonds) instead of a surface. You do not need markers and links for masking, you only need a surface model (meshes true contours false). >>>>> >>>>> Just open the file directly without any options and by default it should make a surface model that you can use in "volume mask" - I thought "meshes true" would still make the surface but maybe it only does that when contours is false. >>>>> >>>>> I'm sorry I mentioned the contours option since it was confusing... I only did so because at first I thought you wanted markers. >>>>> >>>>> I hope this helps, >>>>> Elaine >>>>> ----- >>>>> Elaine C. Meng, Ph.D. >>>>> UCSF Chimera(X) team >>>>> Resource for Biocomputing, Visualization, and Informatics >>>>> Department of Pharmaceutical Chemistry >>>>> University of California, San Francisco >>>>> >>>>> > On Nov 27, 2024, at 1:34 PM, LENKA MILOJEVIC via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> > >>>>> > Dear Dr. Meng, >>>>> > >>>>> > Thank you! I've now managed to open the segmentation with open C:Path format imod meshes true contours true. But If I run volume mask it just outputs: >>>>> > volume mask #3 surfaces #1 fullMap true >>>>> > No surfaces specified >>>>> > volume mask #3 #1 extend 3 >>>>> > Missing required "surfaces" argument >>>>> > volume mask #3 surfaces #1 >>>>> > No surfaces specified >>>>> > >>>>> > Any advice? Is the contour not actually a surface yet? Or am I writing the command wrong. >>>>> > >>>>> > Thank you so so much! >>>>> > >>>>> > Best, >>>>> > Lenka >>>>> > >>>>> > On Wed, Nov 27, 2024 at 1:45 PM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >>>>> > Hi Lenka, >>>>> > The link that you sent is to the Chimera documentation (not ChimeraX): >>>>> > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#object> >>>>> > >>>>> > Since they are different programs, there are differences... but not in this case! ChimeraX can also open these IMOD segmentations: >>>>> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#segmentation> >>>>> > <https://rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html> >>>>> > >>>>> > These segmentation models are surfaces, not the atoms or pseudoatoms (markers) that you would need to define a zone with Color Zone. Although the second link above explains that you can make the IMOD surface mesh into markers/links by opening the file with the "open" command option "contours false," that is unlikely to make them suitable for defining zones. Mainly it is used to improve display. >>>>> > >>>>> > Instead you can use "volume mask" to mask parts of your map with the IMOD segmentation surfaces. >>>>> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask> >>>>> > >>>>> > I hope this helps, >>>>> > Elaine >>>>> > ----- >>>>> > Elaine C. Meng, Ph.D. >>>>> > UCSF Chimera(X) team >>>>> > Resource for Biocomputing, Visualization, and Informatics >>>>> > Department of Pharmaceutical Chemistry >>>>> > University of California, San Francisco >>>>> > >>>>> > > On Nov 27, 2024, at 11:56 AM, LENKA MILOJEVIC via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> > > >>>>> > > Dear Sir or Madam, >>>>> > > >>>>> > > While the 'Input File Types' page lists .mod and .imod files under 3D objects ChimeraX can open, when I try to open a .mod file (e.g., run command open C:/*PathToFile* or through the GUI), the file doesn't show up even though the log output states 'Read IMOD model C:/*PathToFile*, pixel size X'. >>>>> > > >>>>> > > I was wondering if there's any way that I could convert the .mod file into a .cmm file because my goal is to segment a map in ChimeraX using the Color Zone tool, according to the contours from IMOD. >>>>> > > >>>>> > > I appreciate your time and assistance! >>>>> > > >>>>> > > Sincerely, >>>>> > > Lenka >>>>> > >>>>> > _______________________________________________ >>>>> > 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/ >>>>> >>> _______________________________________________ >>> 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/ >>

1 0

IMOD Segmentation to ChimeraX (.mod to .cmm Conversion)
by LENKA MILOJEVIC 27 Nov '24

27 Nov '24

Dear Sir or Madam, While the 'Input File Types' page <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html> lists .mod and .imod files under 3D objects ChimeraX can open, when I try to open a .mod file (e.g., run command open C:/*PathToFile* or through the GUI), the file doesn't show up even though the log output states 'Read IMOD model C:/*PathToFile*, pixel size X'. I was wondering if there's any way that I could convert the .mod file into a .cmm file because my goal is to segment a map in ChimeraX using the Color Zone tool, according to the contours from IMOD. I appreciate your time and assistance! Sincerely, Lenka Lenka Milojević Biophysics PhD Candidate Z. Hong Zhou Lab University of California, Los Angeles

3 10

Closest distance list between residues/atoms; And selecting first/last residue in a chain
by pm676＠cam.ac.uk 27 Nov '24

27 Nov '24

Hi Is there a way by command line to generate a list of residue to residue (or atom to atom) distances ranked by closest to furthest, for say, all residues within 4A of each other at an interface between two protein chains? Can it also state the type of interaction, e.g. salt bridge, H-bond, vdW? Also, completely separately, is there a way by command line to select the first and last residue in a chain (without having to find their number)? No worries if not. Thanks so much! Cheers, Paul

4 14

Visualization of methyls rotations
by Enrico Martinez 27 Nov '24

27 Nov '24

Dear ChimeraX users! In visualizing the MD trajectory, I noticed a small issue with the depiction of the rapid rotations of the ligand's methyl groups. Specifically, the hydrogens appear to periodically collapse into a singularity before returning to their expected positions. Could this be addressed through additional post-processing of the trajectory data? Many thanks in advance Enrico

2 2

Question about using AF3-competitor outputs
by David S. Fay 26 Nov '24

26 Nov '24

Hi, Apologies if this already came up and I missed it. I just ran a few dimer models on the Chai Discovery website (https://lab.chaidiscovery.com/dashboard) and it seems to work quite well. However, when I tried to upload the relevant json file using the Structure Prediction - AlphaFold Error Plot pulldown menu, ChimeraX failed to recognize the file. I tried a few other files and something similar happened. Do you know of a workaround or is this something that is likely to get patched soon? I should mention that Chai may be putting the relevant PAE information into a “npy" file, (e.g., pae.model_idx_0.rank_1.npy) based on the size of that file, and I haven’t yet tried to convert npy to a json or know if that’s even possible. I also wonder if Boltz-1, another AF3 competitor, will have different outputs as well. They don’t seem to have a GUI yet and perhaps they won’t, so I haven’t been able tyo test this yet. I assume this has all been topic of discussions at ChimeraX though… Thanks in advance for your help! David David S. Fay Ph.D. Professor, Department of Molecular Biology Associate Director, National Institutes of Health Wyoming INBRE University of Wyoming email: davidfay(a)uwyo.edu

3 4

How to remove specific H bonds
by Sen, Anindito 26 Nov '24

26 Nov '24

Dear ChimeraX group, How do I remove certain 'H' bonds from an atomic model, leaving the important 'H' bonds Regards Stay safe & Regards Anindito Sen. Ph.D

2 1

Some questions about electrostatic potiential surface
by Quek 26 Nov '24

26 Nov '24

Dear Administrator, May I ask why the electrostatic potential surface I generated in Chimera X is entirely red without any blue? Is it because the electrostatic range is not set correctly? Could you tell me in which module I can set the range for the electrostatic potential? Additionally, how can I display the color scale for the electrostatic potential? Looking forward to your reply. Quek 1171543499(a)qq.com  

2 1

RMSD between nonidentical atomic models
by Roden Deng Luo 26 Nov '24

26 Nov '24

Hi, If two atomic models do not have the exact same atoms, rmsd command does not run. One workaround would be to use matchmaker beforehand, and there is indeed a reported RMSD between "pruned atom pairs." However, this applies the matching before the calculation. In addition, from the attached screenshot (matching https://alphafold.ebi.ac.uk/files/AF-P32565-F1-model_v4.cif to 5wvi chain N), I expect most of the atoms should not be pruned, which is not the case. I wonder if there is a command or tool to calculate the RMSD between the not-moved nonidentical atomic models. Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

2 2

ChimeraX opening failure
by gianmarco.elisi＠gmail.com 25 Nov '24

25 Nov '24

Dear users, ChimeraX fails to open with multiple installation versions. The error with debug option that is shown is the following: Starting main interface Toolshed: find_bundle ChimeraX-Toolbar True None Toolshed: find_bundle ChimeraX-Toolbar True None Toolshed: find_bundle ChimeraX-Toolbar True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-SelInspector True None Toolshed: AvailableBundleCache.load: toolshed_url https://cxtoolshed.rbvi.ucsf.edu Toolshed: AvailableBundleCache.load: url https://cxtoolshed.rbvi.ucsf.edu/bundle/?uuid=e42ced0f-7162-57b1-9d35-4f49e… Toolshed: find_bundle ChimeraX-Core True None Windows fatal exception: access violation Thread 0x00004b9c (most recent call first): File "C:\Program Files\ChimeraX 1.8\bin\Lib\socket.py", line 836 in create_connection File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 945 in connect File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1451 in connect File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 979 in send File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1041 in _send_output File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1281 in endheaders File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1332 in _send_request File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1286 in request File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 1348 in do_open File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 1391 in https_open File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 496 in _call_chain File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 536 in _open File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 519 in open File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 216 in urlopen File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\toolshed\available.py", line 62 in load File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 467 in reload_available File "C:\Program Files\ChimeraX 1.8\bin\Lib\threading.py", line 975 in run File "C:\Program Files\ChimeraX 1.8\bin\Lib\threading.py", line 1038 in _bootstrap_inner File "C:\Program Files\ChimeraX 1.8\bin\Lib\threading.py", line 995 in _bootstrap Current thread 0x00005d04 (most recent call first): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\ui\gui.py", line 315 in event_loop File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\__main__.py", line 1003 in init File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\__main__.py", line 1166 in <module> File "<frozen runpy>", line 88 in _run_code File "<frozen runpy>", line 198 in _run_module_as_main Any suggestion? Thanks

2 1

Overlay of specific chains
by Reza Khayat 25 Nov '24

25 Nov '24

Hi, We have multiple structures of a homo-hexamer (chains A-F). We'd like to overlay limited regions of each chain onto equivalent chains (e.g. residues 200-452 of chain A onto residues 200-452 of chain A). We're having difficulty identifying the correct syntax. Some of our structures align as desired while others are aligned according to the chain combinations that produce the lowest RMSD (e.g. residues 200-452 of chain A align onto residues 200-452 of chain C. Is it possible to restrict which chains align to which? Best wishes, Reza

2 1

VR on Apple silicon?
by David Bhella 22 Nov '24

22 Nov '24

Has anyone managed to make chimeraX VR work on an ARM Mac with meta quest 3? Possible or am I flogging a dead horse? D Professor of Structural Virology Associate Director - MRC-University of Glasgow Centre for Virus Research Director - Scottish Centre for Macromolecular Imaging Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella

2 2

protein void volume or enclosed space
by Vitali James 21 Nov '24

21 Nov '24

Dear Chimera support, Is it possible to calculate the enclosed space, channel volume or void space with the x-ray structure in chimera or chimera x. best, James

3 4

help browser and embedded pdf's
by John Monroe Heumann 21 Nov '24

21 Nov '24

Hi, Am I correct that ChimeraX help browser currently can not automatically open links to pdf's (requiring you to download the file instead)? If so, would this be a reasonable enhancement request or do the pdf reader licensing requirements make it impractical? Thanks! -jh-

3 5

ChimeraX on a tablet ?
by GOVAERTS Cédric 20 Nov '24

20 Nov '24

Hi ChimeraX team I wanted to know if ChimeraX can run on a tablet, either Ipad (M2 or M4 chips) of a Windows tablet (either Intel or Qualcomm Snapdragon) ? Obviously not for using it as main workstation, but rather check structural features while on the move. Thanks Cedric - Prof. Cedric Govaerts, Ph.D. Biochemistry & Structural Biology Universite Libre de Bruxelles - Campus Plaine. Building BC, Room 1C4 203 - Phone :+32 2 650 53 77 Boulevard du Triomphe, Acces 2 1050 Brussels - Belgium

3 6

Adding a Covalently Bound PLP to an AlphaFold Model
by Omar De Bei 20 Nov '24

20 Nov '24

Dear ChimeraX Community, I’m reaching out for advice on what is likely a simple issue, but I’m stuck and would greatly appreciate your input. I’m currently working on a PLP-dependent enzyme and have generated its structure using AlphaFold3. Unfortunately, AlphaFold3 does not include PLP as a preset ligand. To address this, I’m attempting to manually add the PLP to the predicted structure based on homology with other PLP-dependent enzymes. Here’s where I’m facing trouble: The PLP forms a covalent bond with a lysine residue in the active site. After aligning my AlphaFold-predicted structure with the PDB structure of a homologous enzyme, I managed to position the PLP within the predicted structure. However, the lysine residue is not in the correct orientation to form the covalent bond. I’ve tried changing the lysine’s rotamer to improve the position, but it’s still not quite right. I was considering performing a local minimization of the structure to refine the geometry, but I’m unsure how to do this in ChimeraX. Does ChimeraX offer a tool or feature for local minimization that could help in this scenario? If so, could you guide me on how to proceed? Thank you in advance for your help! Best regards, Omar

2 1

Bundle Sample Code
by Lou Holland 19 Nov '24

19 Nov '24

Hello, I work with Jon Agirre at the University of York and am about to start work on developing a privateer bundle for ChimeraX for glycan validation. I have been working through some of the very helpful tutorials and was planning to work through this page as I started building the bundle: https://www.rbvi.ucsf.edu/chimerax/docs/devel/writing_bundles.html I tried to download the sample code ( https://www.cgl.ucsf.edu/chimerax/cgi-bin/bundle_sample.zip) linked in the "Bundle Sample Code" section so that I could use it as a starting point to edit for the privateer bundle, but it seems that the sample code is not currently available. Is this something that you can help with? Best wishes, Lou Holland (Pronouns: they/them) Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK

2 2

Question about commercial license for ChimeraX
by Gleb NOVIKOV 18 Nov '24

18 Nov '24

Dear ChimeraX Development Team, I hope this message finds you well. I am writing as an enthusiastic user of your remarkable software, which has been instrumental in both my academic and educational pursuits. Recently, I was approached by a small company interested in commissioning visualizations as part of a collaborative effort. I would like to inquire whether you offer a specific commercial license suitable for such freelance engagements. Additionally, I would be delighted to contribute to your website by sharing some of my visualizations of molecular systems, should this be of interest to your team. Thank you very much for your time and consideration. I look forward to your response. Best regards, Gleb

2 4

Question the lattest ChimeraX-1.9
by Enrico Martinez 18 Nov '24

18 Nov '24

Dear ChimeraX users! I am testing the new ChimeraX 1.9 release, via creating a short movie demonstrating an X-ray structure with basic features (without molecular dynamics). I noticed that my computer (using an Apple Silicon chip) gets quite hot during the frame rendering process (prior to encoding). In the previous release (1.8), the resource usage didn't seem as intense. Have there been any changes or optimizations in the new version that could explain this increased resource demand? Thank you in advance! Enrico

2 1

Fuzzy colour boundaries in protein cartoon
by James Lingford 18 Nov '24

18 Nov '24

Dear ChimeraX team and users, Is there a way to set colours of individual atoms to have a fuzzy boundary with the surrounding cartoon colour? Example picture attached. Normally, colouring individual atoms will create a solid line between one colour and the next. But is there a setting to change this? Many thanks

2 1

Modelling of missed loop fragments in multi-chain structure
by Enrico Martinez 18 Nov '24

18 Nov '24

Dear Chimera-X users! I need to predict missed loop fragments in a part of a multi-chain complex corresponded to GPCR bound to heteromeric G-protein (pdb id 8HTI). In this structure the chain A (a subunit of the G-protein) contain missed loop fragments. So the following commands were executed in command line to reconstruct the entire structure of this subunit: open 8hti seq chain /A ui tool show "Model Loops" modeller refine 1/A:1:internal-missing numModels 5 fast false adjacentFlexible 1 protocol standard which very slowly produces 5 models of the chain A. The problem was that the modeller considered the chain A in isolation from the rest of the structure and predicted loops overlapped with other chains of the G protein. Would it be possible to reconstruct the missing fragments in the chain A considering also the presence of other chains to build the full complex ? Many thanks in advance Enrico

3 15

adding a hydrogen to side chain of Glu
by Chang Jang 15 Nov '24

15 Nov '24

Hi ChimeraX users, I am building a customer peptide containing Glu, Ala, Lys using Build Structure. Once I built it, I added hydrogens. But, one oxygen in the side chains of Glu does not have a hydrogen added. How would I fix the structure? Thanks, Chang

2 2

2 different clipping planes, 1 per model?
by Vincent CHAPTAL 15 Nov '24

15 Nov '24

Hi, I wonder if it is possible to have 2 different clipping planes, 1 per model? It would be nice to show an helix as a surface within a domain like this. Thanks 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/

2 1

the artifacts of the PBC of the MD trajectory
by Enrico Martinez 14 Nov '24

14 Nov '24

Dear Chimera-X users ! I am visualizing an MD trajectory of a biomembrane system obtained from Amber MD using the autoimage method of cpptraj. However, in this trajectory, I still observe very rapid lateral diffusion of certain lipids, which cross the entire system too quickly. Is there a way in ChimeraX to hide or suppress such motions for selected atomic groups (e.g., lipids)? Many thanks in advance Enrico

4 10

AlphaFold 3 source code released today
by Tom Goddard 11 Nov '24

11 Nov '24

AlphaFold 3 source code was released today AI protein-prediction tool AlphaFold3 is now open source <https://www.nature.com/articles/d41586-024-03708-4> https://github.com/google-deepmind/alphafold3 It is for non-commercial use only, and they require you to submit a form and get approved (2-3 days) to get the parameters. Tom

1 0

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

11 Nov '24

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

5 16

New user -have queries
by karan kohli 11 Nov '24

11 Nov '24

Hi, Thank you for developing Chimera X, a tool that can help novices like myself to make in silico predictions. I am new to the world of silico protein interaction prediction. I am looking to use Chimera X to predict interaction between the antibody clones our company generated and the target protein. This should be doable with Chimera X right. I I am not sure how to do it. I am trying to follow the below video., But I am struggling to enter my ab sequence as it contains two chains (heavy and light). https://www.youtube.com/watch?v=TMcjEecFHaI I would really appreciate some help. Thank you, Karan

2 1

isolde write phenixRsrInput – how to restrain ligands?
by Shahid, Taha (Dr.) 08 Nov '24

08 Nov '24

Hi Tristan, I am trying to phenix real-space refine a structure containing AMPPNP, which I have modelled very accurately with ISOLDE. I create inputs using the isolde write phenixRsrInput command, including the restrainPositions true and includeHydrogens true arguments (which normally works perfectly). However, in this case, the Rsr output yields AMPPNPs with bond-length RMSZs > 2, although this is not the case in the input model itself. Would you be able to advise as to how I can potentially restrain the AMPPNP heavy atoms from the ISOLDE model as well? I am not a phenix expert, so not having to create these manually would be ideal. Perhaps a phenix command that will automatically generate an appropriate restraints file (to append to the isolde write phenixRsrInput command or phenix.real_space_refine itself), and/or lines that may be added to the real_space_refine.eff file created by ISOLDE? Any help would be immensely appreciated. Best regards, Taha

3 3

Re: [Chimera-users] Write out SeqRes entry
by Eric Pettersen 07 Nov '24

07 Nov '24

Hi David, For PDB output, ChimeraX should output SEQRES records for each chain as long as either: (A) the chain had sequence information in the original input file (e.g. SEQRES records), or (B) the chain has no missing-structure pseudobonds. I not the author of the mmCIF I/O part of ChimeraX, but I believe the criteria is different in that the chain has to have its "full_sequence_known" attribute set to true. You can do this "by hand" with the command (assuming your structure is model #1) "setattr #1 chains full_sequence_known true". --Eric Eric Pettersen UCSF Computer Graphics Lab P.S. There are different lists for Chimera vs. ChimeraX questions. I have cc'ed the ChimeraX list on this. > On Nov 6, 2024, at 10:54 AM, David Bhella via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera/ChimeraX team, > > I have a model for an asymmetric unit of a virus capsid that has three chains of the same capsid protein – but I am having trouble depositing my model in the PDB because it only has a seqres entry for one of the three chains (B). Whatever I do, chimeraX will only write entries for that chain. Is there a way to force chimeraX (or any other program) to write the seqres card for each chain correctly? > > Thanks > D > > David Bhella > Professor of Structural Virology > Director, Scottish Centre for Macromolecular Imaging > Associate Director, MRC - University of Glasgow Centre for Virus Research > +44 (0)141 330 3685 <tel:+441413303685> > > > > > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

3 2

Command to measure the Atomic to Map fit quality
by Roden Deng Luo 06 Nov '24

06 Nov '24

Hi ChimeraX Team, I wonder if there is a command that can measure the fit quality of an atomic structure to a volume map. I imagine the metric could be the sum of the density of all atoms or a correlation. Something like: fit_quality #ModelID in #VolumeID (similar to: rmsd #1 to #2). Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

4 6

Error saving a chimeraX session for large MD trajectory
by Enrico Martinez 06 Nov '24

06 Nov '24

Dear ChimeraX users! Dealing with the session contained loaded md trajectory of 10000 snapshots for a quite big system I got the following error trying to save this session File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101, in provider_save saver_info.save(session, path, **provider_kw) File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 922, in save session.save(output, version=version, include_maps=include_maps) File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 651, in save fserialize(stream, data) File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py", line 76, in msgpack_serialize stream.write(packer.pack(obj)) ^^^^^^^^^^^^^^^^ File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 285, in msgpack._cmsgpack.Packer._pack File "<stringsource>", line 69, in cfunc.to_py.__Pyx_CFunc_8chimerax_4core_10_serialize_object__lParenobject__rParen_to_py_3obj.wrap File "src/_serialize.pyx", line 253, in chimerax.core._serialize._encode_ext File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 264, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 285, in msgpack._cmsgpack.Packer._pack File "<stringsource>", line 69, in cfunc.to_py.__Pyx_CFunc_8chimerax_4core_10_serialize_object__lParenobject__rParen_to_py_3obj.wrap File "src/_serialize.pyx", line 226, in chimerax.core._serialize._encode_ext File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack ValueError: bytes object is too large ValueError: bytes object is too large File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack *See log for complete Python traceback.* Would it be possible to reduce the number of frames loaded as coordset e.g. closing the last 6000 frames ? Many thanks in advance! Enrico

2 4

Generating quantitative values for electrostatic potential and molecular lipophilicity potential
by mishra.ananya.163＠gmail.com 06 Nov '24

06 Nov '24

Dear Sir/Madam, I hope this message finds you well. My name is Ananya, and I am an undergraduate student working on a project analysing protein structures. I am currently exploring the tools available in ChimeraX to measure structural parameters of protein models. I find the visualization features for surface electrostatic potential and molecular lipophilicity potential especially valuable for my research, as they provide essential insights for my analyses. However, I have encountered some difficulty in locating a way to export quantitative values for these surface properties. Could you please advise if there is a method within ChimeraX to generate and export these values? Thank you for your time and I would greatly appreciate any guidance you could offer. Hope you have a great day ahead! Best regards, Ananya

3 8

integration of US-align into ChimeraX
by Chengxin Zhang 06 Nov '24

06 Nov '24

Dear ChimeraX developer. I am the developer of the US-align tool for protein and nucleic acid structure alignment. We currently offer a command line tool and a plugin for PyMOL. We are asked by the community to make a ChimeraX plugin. I have used ChimeraX for cryo-EM structure analysis before and know that there is a related tool called matchmaker. However, I do not know where to start to implement a matchmaker-like plugin for US-align in ChimeraX. Can you give me some recommendations and/or point me to a developer I can work with? Thanks. Chengxin Zhang, PhD Research Assistant Professor Department of Computational Medicine & Bioinformatics University of Michigan, Ann Arbor, MI

2 1

Variables and conditional statements in the command line
by Roden Deng Luo 05 Nov '24

05 Nov '24

Hello again, Are variables and conditional statements possible in the command line in any way? Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

2 2

Troubleshooting the match function
by Christman, Nick 04 Nov '24

04 Nov '24

Hello, My name is Nick Christman and I am a microbiology PhD student at Indiana University. I am using ChimeraX to visualize and compare some small proteins (minor pilins) and it has been working great. I have run into an issue that I am hoping you can help me resolve. I want to use the match function to compare various different minor pilins. Each minor pilin has a somewhat unique structure, and I am trying to make the case that certain minor pilins from one organism are homologous to other minor pilins from a different organism. I have noticed that the match function provides different results from session to session. This concerns me and makes me question how much I can trust the results provided by chimeraX. Along with different spatial matching, the calculated RMSD values differ greatly. Is there a way I can make these matches more consistent? Like dictating a set starting point for matching? Thanks for your time! Nick Christman (He/Him) Dalia Lab Indiana University

2 1

setzoom command in Chimera X
by Vitali James 04 Nov '24

04 Nov '24

Dear Chimera support, There was a some old code to set the zoom in the chimera. I would like to set the same frame size of different models and different views in chimerax. How it can be done in chimeraX. best, James

2 1

Tool docking
by Eric Pettersen 01 Nov '24

01 Nov '24

Hi all, Starting with tomorrow’s daily build (but not the 1.9 release candidate or [eventual] production release), most tools can no longer be docked into the top or bottom areas of the main window, just the sides. This should prevent a lot of accidental grief from accidentally docking a tool into the toolbar area. This policy can be overridden by the tools themselves if typical use of that tool might involve docking into the top or bottom areas. Initially, two tools override the policy: the sequence viewer can be docked anywhere (since you might want it as wide as possible), and the tool created by the buttonpanel command can be docked into the top area, so that it can be placed next to the toolbar. If there are other tools that can really benefit from being docked into the top or bottom areas, please let me know. --Eric Eric Pettersen UCSF Computer Graphics Lab

2 2

Using name of selection with rmsd command
by Alexander Lee 01 Nov '24

01 Nov '24

Hello! I've been trying to use "sel sel res t; ~sel H; ~sel @N,CA,C,O; name target sel; sel #2:23; ~sel H; ~sel @N,CA,C,O; name original sel; rmsd target to original" to find the RMSD of just the target's side chain to the original, but I keep getting a reported RMSD of 0.000. I click on an atom of the target residue, then use "sel sel res t" to select the whole residue, "~sel H" to deselect hydrogens, " and "~sel @N,CA,C,O" to deselect the backbone. I then name the left-over selections. I thought this series of commands would work but it's giving me an incorrect RMSD. Is there a different combination I should try? Thank you, Alex

2 2

Coloring surface patches
by Radoslav Krivak 31 Oct '24

31 Oct '24

Hi I'm struggling with the following task. I want to display protein surface and color specific surface patches. More precisely, I want to: For each surface patch: 1. select specific solvent exposed atoms (by "Atom serial number" column from pdb file) 2. assign their surface a custom color (different color for each patch) A surface patch can contain atoms from 2 or more chains. Basically I'm trying to achieve something that looks like this: https://raw.githubusercontent.com/rdk/p2rank/refs/heads/develop/misc/img/p2… Is that even possible in ChimeraX? If it's not possible to select specific atoms by atom serial number I'd like to do it at least for residues. I’d be grateful for any help. Best regards Radoslav Krivak

2 1

Re: Smooth-MD script for a trajectory visualisation
by Enrico Martinez 29 Oct '24

29 Oct '24

Hello Eric, Just one extra question about the Smooth-MD script :-) Would it be possible to extend the idea of different smooth windows on different selections within the same model id (besides the version that we discussed applying for several different models).. For example, I have a complex system composed of membrane protein bound to a ligand embedded in explicit water and lipids. So, I divided all the components according to three different selections, which I would like smooth differently, in the following way: 1) protein & ligand (protein | :LIG) --> smooth with 5 windows 2) lipids according to amber naming (:PC,PE,PS, OL,PA) smooth with 6 windows 3) water and ions (:WAT|:NA*|:Cl*) smooth with 7 windows Would it be possible to do such tricky things using the same script? Many thanks in advance ! Enrico Il giorno sab 19 ott 2024 alle ore 02:55 Eric Pettersen <pett(a)cgl.ucsf.edu> ha scritto: > Hi Enrico, > Our servers have been down this week, so this is my first opportunity to > respond. So one possible approach is to change the "window = 10" line to: > > window_by_id = { (1,): 5, (2,): 10 } > > and change the 'if/continue' statement just inside the loop to: > > try: > window = window_by_id[s.id] > except KeyError: > continue > > The 'id' attribute of a model is a tuple of the model ID numbers, so for > model #1 it would be (1,), for model #2.2.1 it would be (2,2,1), etc. > So the try/except clause skips all models other than the ones you > explicitly put in the window_by_id dictionary. > > --Eric > > On Oct 11, 2024, at 1:32 PM, Enrico Martinez <jmsstarlight(a)gmail.com> > wrote: > > Hello Eric, > > I have an extra question about the Smooth MD script: I modified it abit to > apply the smoth effect only on a model with the name "ottimo.pdb" so that > it will affect only one selected model ( in the case when there are several > models in the same session ..) Here is this version enclosed. > > Could you suggest how it could be further modified to affect e.g. 2 models > via 2 different smooth windows e.g. smooth the model with the id 1 window=5 > and smooth the model with the id 2 with window2=10 ? > > Many thanks for help! > > Enrico > > Il giorno ven 8 dic 2023 alle ore 16:10 Enrico Martinez < > jmsstarlight(a)gmail.com> ha scritto: > >> Thank you very much Eric ! >> >> Cheers >> >> Enrico >> >> Le mer. 6 déc. 2023 à 19:02, Eric Pettersen <pett(a)cgl.ucsf.edu> a écrit : >> >>> Hi Enrico, >>> I have updated the smoothing script on the Scripts >>> <https://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts> page. If you get >>> a new version, there is a line near the top ("stride = 1") that you can >>> edit to make it use, say, every 5th frame ("stride = 5"). One issue is >>> that the coordinate set slider doesn't properly react to the change in the >>> number of frames. You have to close the slider and open a new one >>> ("coordset slider #1"). I will look into fixing that. >>> >>> --Eric >>> >>> On Dec 6, 2023, at 1:34 AM, Enrico Martinez via ChimeraX-users < >>> chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> and generally it would be visually fine with averaging of every N frame ? >>> well it would be interesting to test anyway :-) >>> >>> Cheers >>> >>> Enrico >>> >>> Il giorno mar 5 dic 2023 alle ore 19:30 Eric Pettersen >>> <pett(a)cgl.ucsf.edu> ha scritto: >>> >>> >>> Well, the smoothing script temporarily takes about triple the memory use >>> of the baseline trajectory, so I can imagine it crashing for a large >>> trajectory. Do you need 1000 frames? I could change the script to use >>> every Nth frame, which would use a lot less memory... >>> >>> --Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>> >>> On Dec 5, 2023, at 7:13 AM, Enrico Martinez via ChimeraX-users < >>> chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> update: I've just got a crash with md-smooth py script on chimera-x >>> working on a big system with > 1000 frames loaded in a single pdb >>> (with smaller trajectory there is no issues ..) >>> >>> Enrico >>> >>> Il giorno mer 15 nov 2023 alle ore 18:53 Eric Pettersen >>> <pett(a)cgl.ucsf.edu> ha scritto: >>> >>> >>> You are welcome. >>> >>> I don't think there is a "right" value for the window. A larger value >>> will provide more smoothing, while also creating more non-physical >>> geometries for highly mobile parts of the structure. A judgement call >>> really. >>> >>> --Eric >>> >>> On Nov 15, 2023, at 3:33 AM, Enrico Martinez via ChimeraX-users < >>> chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> Gotcha, thank you very much Eric ! >>> >>> BTW what is the value for the window that should be used ? Does it >>> mean that the higher value would result in smoother dynamics ? >>> >>> Enrico >>> >>> Il giorno mar 14 nov 2023 alle ore 19:47 Eric Pettersen >>> <pett(a)cgl.ucsf.edu> ha scritto: >>> >>> >>> Hi Enrico, >>> I don't see how you could get that error. I couldn't reproduce it >>> myself. I would need some kind of recipe for how you get it to occur. A >>> separate problem is that the averaging in the script isn't really right. >>> Line 21 of the script should be changed from: >>> >>> weight = window + 1 + abs(i-j) >>> >>> to: >>> >>> weight = window + 1 - abs(i-j) >>> >>> i.e. change the "+ abs(...)" to "- abs(...)". I have corrected the >>> script on the Scripts page. >>> >>> --Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>> >>> On Nov 14, 2023, at 6:31 AM, Enrico Martinez via ChimeraX-users < >>> chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> update: i've just opened closed chimera-x and reloaded my pdb and >>> everything works as expected. probably there is a bug somewhere .. >>> >>> Il giorno mar 14 nov 2023 alle ore 14:56 Enrico Martinez >>> <jmsstarlight(a)gmail.com> ha scritto: >>> >>> >>> 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 >>> >>> _______________________________________________ >>> 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/ >>> >>> >>> >>> _______________________________________________ >>> 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/ >>> >>> >>> >>> _______________________________________________ >>> 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/ >>> >>> >>> >>> _______________________________________________ >>> 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/ >>> >>> >>> >

2 2

Sequence alignment and Extraction
by Mamadou Sangare 25 Oct '24

25 Oct '24

Dear, I would like to align two protein structures A and B, select and extract the parts of the B sequence that match A in a fasta file. Thank you for your support.

2 1

Visualisation of water near protein
by Enrico Martinez 25 Oct '24

25 Oct '24

Dear Chimera X users ! I have a question about the visualization of water around the protein. When I open the pdb + trajectory of the whale system, ChimeraX masks most of the water box, only showing some selected water molecules (probably involved in the interactions with the protein). Then, viewing the MD system, I can observe an exchange of this water, which is great ! Would it be possible via some command to modify the number of the displayed water in the beginning of simulation e.g. showing more water observed in the proximity to protein (..but still not the whole water box !) ? Many thanks in advance Enrico

2 4

Coloring by attribute
by Murugesh Narayanappa 24 Oct '24

24 Oct '24

Hi, I am Murugesh, a postdoctoral fellow in Dr. Rajat Rohatgi’s lab at Stanford University. I created an attribute file using z-scores and mapped these scores onto a structure, applying a gradient color scheme. However, I would like to know if there's a way to use discrete colors instead. Specifically, I want to apply a single color with uniform intensity for a selected range of z-scores (e.g., from 3 to 10) rather than using a gradient. I haven’t been able to figure this out. Is there an option or command I can try? I would appreciate any guidance. Thank you, Murugesh

2 2

Re: Inquiry About Translating ChimeraX GUI Language
by Zach Pearson 24 Oct '24

24 Oct '24

I think that was meant for Tom, I barely said anything, but thank you on his behalf and good luck with your translation project! We’re excited to see it. — Zach > On 24 Oct 2024, at 00:14, 刘俊骅 <273667986(a)qq.com> wrote: > > Dear Zach, > Thank you very much for your detailed and clear response. The direction you provided has been extremely helpful and will enable me to delve deeper into understanding these projects. I am excited to explore the code and see how I can customize the GUI interface to better suit my needs. > Your guidance has given me a great starting point, and I appreciate the time and effort you have invested in helping me. Your support is greatly appreciated, and it reinforces my enthusiasm for working with ChimeraX. > Once again, thank you for your assistance and for developing such an outstanding tool. Your work is truly making a significant impact on the scientific community. > Best regards, > Junhua Liu > > ------------------ 原始邮件 ------------------ > 发件人: "Zach Pearson" <zjp(a)cgl.ucsf.edu>; > 发送时间: 2024年10月23日(星期三) 凌晨2:35 > 收件人: "刘俊骅"<273667986(a)qq.com>; > 抄送: "ChimeraX Users Help"<chimerax-users(a)cgl.ucsf.edu>; > 主题: Re: [chimerax-users] Inquiry About Translating ChimeraX GUI Language > > A very cursory googling for ‘PyQt multilanguage’ brings up this repo: https://github.com/yjg30737/pyqt-multi-language-example but it is for PyQt5. > > Feel free to fork the ChimeraX repository and make pull requests. We would be eager to learn how to do this and turn it into a community-driven project. > > — Zach > > > On 22 Oct 2024, at 11:14, Tom Goddard via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Hi Junhua, > > > > That would be great to add some Chinese language support in ChimeraX. We haven't looked into supporting languages other than English, but there are many Chinese speaking ChimeraX users. ChimeraX uses the Qt window toolkit which has "internationalization" support. Specifically ChimeraX uses the Python interface to Qt, called PyQt. If you figured out how to customize the ChimeraX GUI text we'd be interested in including that in ChimeraX. Your ChiimeraX distribution includes all the Python code which creates the user interface, so you could experiment with just changing the Python code in your distribution. The ChimeraX code is also on Github here > > > > https://github.com/RBVI/ChimeraX > > > > Here is the place in the code where the top level File, Edit, Select, Actions, Tools, ... menus are created. > > > > https://github.com/RBVI/ChimeraX/blob/1f1a0512d53424163992b53eadeffd2d9e39d… > > > > I guess the individual menu entries are added in many places in the code. For instance the File / Open... entry is here > > > > https://github.com/RBVI/ChimeraX/blob/1f1a0512d53424163992b53eadeffd2d9e39d… > > > > and it uses the add_menu_entry() function which probably is used to add all the menu entries > > > > https://github.com/RBVI/ChimeraX/blob/1f1a0512d53424163992b53eadeffd2d9e39d… > > > > Let us know what you figure out. > > > > Tom > > > > > >> On Oct 22, 2024, at 9:36 AM, 刘俊骅 via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > >> > >> Dear UCSF ChimeraX Developers, > >> I hope this email finds you well. > >> Firstly, I would like to express my sincere gratitude for developing such a powerful and versatile software as UCSF ChimeraX. It has been an invaluable tool for my research and visualization needs. > >> I have a question regarding the translation of the GUI interface language. I am interested in translating the interface into another language. Since I noticed that UCSF ChimeraX is based on Python, I was wondering if it is possible to modify certain .json, .py, or .xml files to change the displayed language. My intention is purely for personal use, and I have no plans to distribute or profit from any modifications. > >> Could you please provide any guidance or resources on how to achieve this? Any pointers or documentation would be greatly appreciated. > >> Thank you very much for your time and consideration. > >> Best regards! > >> Junhua Liu 273667986(a)qq.com > >> _______________________________________________ > >> 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/ > > > > _______________________________________________ > > 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/

1 0

Inquiry About Translating ChimeraX GUI Language
by 刘俊骅 24 Oct '24

24 Oct '24

Dear UCSF ChimeraX Developers, I hope this email finds you well. Firstly, I would like to express my sincere gratitude for developing such a powerful and versatile software as UCSF ChimeraX. It has been an invaluable tool for my research and visualization needs. I have a question regarding the translation of the GUI interface language. I am interested in translating the interface into another language. Since I noticed that UCSF ChimeraX is based on Python, I was wondering if it is possible to modify certain .json, .py, or .xml files to change the displayed language. My intention is purely for personal use, and I have no plans to distribute or profit from any modifications. Could you please provide any guidance or resources on how to achieve this? Any pointers or documentation would be greatly appreciated. Thank you very much for your time and consideration. Best regards! Junhua Liu 273667986(a)qq.com

5 6

Running_chimera_in_R
by Eric Pettersen 23 Oct '24

23 Oct '24

> From: Bipasa Show <bipasa.show22ug(a)apu.edu.in> > Subject: Running_chimera_in_R > Date: October 21, 2024 at 10:48:18 PM PDT > To: chimerax-users(a)cgl.ucsf.edu > > > Dear Team Chimera X, > Hope this email finds you well. I am reaching out in order to know if there is a way I can use R to automate specific processes in Chimera and Chimera X like structure-based sequence alignment, finding SASA for multiple residues etc. . It would be nice if you could let me know if automation in these softwares are possible using R. > Thanks and regards, > Bipasa

2 2

Problem with the coulombic protein
by svle＠tiscali.it 23 Oct '24

23 Oct '24

Hi, I have six representative frames, in pdb format , of six clusters evaluated with cpptraj of a trajectory . For three representative frames the command "coulombic protein" the surface is produced without any problem whereas for the remaining three I receive errors similar to the following text: coulombic protein Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue CYM (net charge -1) with am1-bcc method Running ANTECHAMBER command: /usr/lib/ucsf-chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /tmp/tmp76d1_frw/ante.in.mol2 -fi mol2 -o /tmp/tmp76d1_frw/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n (CYM) (CYM) Welcome to antechamber 20.0: molecular input file processor. (CYM) (CYM) Info: Finished reading file (/tmp/tmp76d1_frw/ante.in.mol2); atoms read (22), bonds read (21). (CYM) Info: Determining atomic numbers from atomic symbols which are case sensitive. (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (CYM) (CYM) (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (CYM) Info: Total number of electrons: 94; net charge: -1 (CYM) (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out (CYM) (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1 (CYM) (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC (CYM) Charges for residue CYM determined Assigning partial charges to residue CYM (net charge -1) with am1-bcc method CYM: number of electrons (92) + formal charge (-1) is odd; cannot compute charges for radical species using AM1-BCC method Any suggestions to solve this problem? Thanks. Saverio

2 4

Re: Mercator projection of MRC voluem coloured by attribute
by Tom Goddard 23 Oct '24

23 Oct '24

Hi Pranav, The image in my last email was created useing the 5 commands I listed in that email. The main drawback is it gives a 360 view from a point at the middle of the map looking out. So it can be used to see what the inside of a virus capsid looks like, but not the outside. My other suggestion about combining strips of a thousand images during a rotation is what would allow getting an outside 360 degree view. Tom > On Oct 23, 2024, at 10:40 AM, Pranav Shah <pranav.shah(a)strubi.ox.ac.uk> wrote: > > Love it! Thanks Tom, this might just work. WOuld you be happy to share the script you used to generate that stretched out view? > > > Best, > Pranav > -- > Pranav Shah > Post-doctoral Research Associate (PDRA) > Division of Structural Biology (STRUBI) > University of Oxford. > Center for Human Genetics, > Roosevelt Drive, > Oxford, OX3 7BN, UK > > ________________________________________ > From: Tom Goddard <goddard(a)sonic.net> > Sent: 22 October 2024 20:19 > To: Pranav Shah > Cc: ChimeraX-bugs(a)cgl.ucsf.edu > Subject: Re: [chimerax-users] Mercator projection of MRC voluem coloured by attribute > > Hi Pranav, > > I guess you mean you want to save a 360 degree projection image of your colored map? There is nothing quite like that in ChimeraX. If you want a 360 view from the center of the map you can get that with "camera 360" after positioning the view point in the middle of the map. For example > > open 1080 from emdb > color cylindrical #1 palette redblue > move z 350 > turn x 90 center #1 > camera 360 > > There is also command volume unroll that can unroll a cylindrical map. But it does not preserve coloring. And there was a flatten icosahedron capability that worked with atomic models in Chimera that is not in ChimeraX. > > https://www.cgl.ucsf.edu/chimera/experimental/flatten_icosahedron/flaticos.… > > For what you want you could spin the model around 360 degrees recording images each 0.2 degree, then have a script take the center column of pixels from each image and lay those columns side-by-side in a single image 1800 pixels wide. > > Tom > > Example of camera 360 giving view inside map EMDB 1080. > [emd1080.png][emd1080_360.png] > > On Oct 22, 2024, at 10:51 AM, Pranav Shah via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > hi Team, > This is potentially a left-of-center question, but is there a way I > could generate a mercator projection of an MRC volume that I have > colored by zone? I am happy to code this up in the chimerax python > environment, but I am not sure how I could access the voxel colour > information before projecting the volume. > > 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 > _______________________________________________ > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ > >

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Installing plugins not working
by Oliver Clarke 23 Oct '24

23 Oct '24

Hi, Since the website came back, I can't get installing external tools (e.g. Clipper, ISOLDE) to work - is it just me or down for others also? It says it is downloading the bundle when I click install, but nothing happens after that. Cheers Oli

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Mercator projection of MRC voluem coloured by attribute
by Pranav Shah 22 Oct '24

22 Oct '24

hi Team, This is potentially a left-of-center question, but is there a way I could generate a mercator projection of an MRC volume that I have colored by zone? I am happy to code this up in the chimerax python environment, but I am not sure how I could access the voxel colour information before projecting the volume. 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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placing a model at points defined in a CMM file
by Pranav Shah 22 Oct '24

22 Oct '24

hi Team, In addition to my previous question, is there a chimeraX function I could leverage to translate a pdb model to a point defined in a CMM file? 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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Viewing ccp4 volume data - Hiding outline box volume outside surface
by Stylianos Iliadis 22 Oct '24

22 Oct '24

Hello, I want to visualise a surface (isosurface) loaded from a ccp4 file on top of a protein binding site. When I load the volume and adjust the level properly, I can see the “correct” surface (visualised usually on Pymol), but this is only possible when I view slices of the volume=cube box. If I don’t use the sliced view, I only see a cube. Essentially, my question is how can someone hide the “negative” volume inside the cube box that is not part of the depicted isosurface? Thanks, Best, Stel Iliadis

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Named selection problem
by Patrick Moynihan 22 Oct '24

22 Oct '24

Hi, I was hoping someone could help me with a persistent problem I am having. I am running ChimeraX version 1.8 (2024-06-10) on OSX. This problem has persisted for quite a while through several versions. If I work in ChimeraX and save a group of atoms as a named selection, it generally works as expected for the first group. After that, if I use the command “name XXXX” or define a selection via the GUI, it seems to take the input and reserve the name. However, when I return and select that named selection, the entire protein gets selected. I cannot for the life of me figure out why. I’ve tried low numbers of atoms and high, short names and long, the problem persists. Any advice would be appreciated. Thanks, Patrick

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Set transparency of multiple models
by Ioannis Skalidis 22 Oct '24

22 Oct '24

Dear ChimeraX mailing list, I was wondering if there is a command to set the alpha (transparency) of multiple models (not maps). So far, I know that this is possible for maps through the transparency command, but the only way I know of to make a model transparent is to set each model alpha value individually in its color panel. Thanks for your help! Cheers, Dr. Ioannis Skalidis | Structural Biochemist | Twitter: @imjohnskal <https://twitter.com/imjohnskal> | johnskalidis(a)gmail.com

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Query regarding Chimerax capablities
by Joseph Clifford 21 Oct '24

21 Oct '24

Hi Team, I hope this email reaches you well. I am a R&D scientist at Randox Laboratories and was wondering if possible could you model the nicked free form of PSA with the additional 7 amino acids at the N-term. I am exploring the capabilities of chimerax and want to put a business case together to my manager regarding this software application. [cid:54b7fcba-418a-438f-a6b0-5358e796c896] Many thanks in advance, Joseph Clifford This e-mail and any attachments are confidential and intended solely for the addressee and may also be privileged or exempt from disclosure under applicable law. If you are not the addressee, or have received this e-mail in error, please notify the sender immediately, delete it from your system and do not copy, disclose or otherwise act upon any part of this e-mail or its attachments. E-mail communications are not guaranteed to be secure or virus-free. Therefore Randox does not accept responsibility for any loss arising from unauthorised access to, or interference with, any e-mail communications by any third party, or from the transmission of any viruses. Randox does not accept liability for any errors or omissions in the contents of this message which arise as a result of e-mail transmission. Replies to this e-mail may be monitored by Randox for business and operational purposes. Any opinion or other information in this e-mail or its attachments that does not relate to the business of Randox is personal to the sender and is not given or endorsed by Randox.

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Inquiry on Setting Clipping Caps for Helix in Cylinder Visualization
by youngxiaolin 18 Oct '24

18 Oct '24

Dear Sir/Madam, I am currently working on a cross-sectional visualization of a transmembrane helix bundle shown as cylindrical cartoon. I notice that, unlike in surface visualizations, my helices are not capped, leaving the ends exposed. Are there specific parameters or settings within ChimeraX that I should adjust to customize the appearance of the helix caps? Thank you in advance for your assistance. I am looking forward to your expert advice. Best regards, Xiaolin Yang National clinical research center for Infectious diseases

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Issues accessing your websites
by Karp Mike (External) 18 Oct '24

18 Oct '24

Hi, We've been trying to install a chimerax plugin over the last few weeks and noticed we were unable to access the webpage the application tries to open (ChimeraX Toolshed). We checked and found this wasn't accessible from multiple internet connections. I've since noticed we are also unable to access any content on https://cgl.ucsf.edu Are you aware of an issue with your web sites? Regards, Mike. ________________________________ Legal Notice: This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. UCB screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. UCB accepts no liability for any damage caused by any virus transmitted by this electronic mail. (Ref: #*UG1107) [Ref-UG1107] ________________________________

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Fwd: 3d glasses free monitors from acer....
by Tom Goddard 18 Oct '24

18 Oct '24

Hi Krish, Ok. I fixed the first error which was caused by the Acer display OpenXR saying it did not have valid position and orientation data for the viewer. ChimeraX did not handle that correctly since VR headsets never have that problem. It might mean that eye tracking of the Acer display did not see your eyes so it did not know your viewing position. Or it could mean the Acer display never provides both position and orientation. If it never provides position and orientation of the viewer then the fixed code still won't render anything and we'll have to do more work to figure out how you are are supposed to get the view direction. The fixed XR code will be in daily builds dated October 17, 2024 or newer. Tom > > >> On Oct 16, 2024, at 2:53 PM, Krishnan Raman <RKrishnan(a)BIOCRYST.com> wrote: >> >> Hi Tom, >> I am willing it work with it till it gets resolved. It might open the display for other applications as well. >> Thanks again for your prompt responses. >> krish >> >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Wednesday, October 16, 2024 4:14 PM >> To: Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> >> Subject: Re: [chimerax-users] 3d glasses free monitors from acer.... >> >> [EXTERNAL] >> >> Hi Krish, >> >> That is some progress. I see why ChimeraX gives that error. It is looking for if the OpenXR connected device does both position and orientation tracking (for VR headsets) and your display says it doesn't do at least one of those and then the ChimeraX code breaks. I may be able to fix that and see if you get further. I say "may" because the ChimeraX code is designed for VR where the headset has a position and orientation in space that is reported. If the Acer display doesn't give a position and orientation for the person's head using its eye tracking then the ChimeraX code would need to do something different to decide the view point. If I had a display I could explore it, but without one it will be hard to figure out. If you want to replace some ChimeraX Python code I can give you some that will help figure out the issues, but it may take a lot of back and forth of you trying code to get anywhere. >> >> Tom >> >> >> >> On Oct 16, 2024, at 1:40 PM, Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> wrote: >> >> SpatialLabs User Guide (acer.com) <https://link.edgepilot.com/s/e6a7c1ed/uvnt1Jd_IECk7VUP7-Ti6Q?u=https://spat…> >> >> <image001.png> >> >> Also, >> Tried XR on. The display froze but did go into the 3D mode. Chimerax is recognizing the driver and the monitor. I got an error while reporting this bug. So pasting it here. >> >> >> An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command "graphics restart" after changing the settings that caused the error. >> >> 'XR' object has no attribute '_eye_view_states' >> >> Traceback (most recent call last): >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\core\updateloop.py", line 84, in draw_new_frame >> view.draw(check_for_changes = False) >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\graphics\view.py", line 188, in draw >> self._draw_scene(camera, drawings) >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\graphics\view.py", line 231, in _draw_scene >> camera.set_render_target(vnum, r) >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\vive\xr.py", line 941, in set_render_target >> self._start_rendering() >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\vive\xr.py", line 796, in _start_rendering >> if not xr.start_frame(): >> ^^^^^^^^^^^^^^^^ >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\vive\openxr.py", line 372, in start_frame >> self._end_xr_frame() >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\vive\openxr.py", line 446, in _end_xr_frame >> eye_view = self._eye_view_states[eye_index] >> ^^^^^^^^^^^^^^^^^^^^^ >> AttributeError: 'XR' object has no attribute '_eye_view_states' >> >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Wednesday, October 16, 2024 12:10 PM >> To: Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> >> Cc: Greg Couch <gregc(a)cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>>; ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> >> Subject: Re: [chimerax-users] 3d glasses free monitors from acer.... >> >> [EXTERNAL] >> >> Hi Krish, >> >> I would hope the Acer SpatialLabs 3D display could render with the standard sequential stereo used with old LCD shutter glasses or polarized glasses systems. ChimeraX can output that using command "camera stereo". But I didn't seen any indication in searching online that they support that. Nor did I see any mention of them supporting the standard side-by-side stereo format which ChimeraX can also output (camera sbs). I would think the display would handle these format because 3D games use those. How could they not make it work with 3D games? What I did see online is that it works with OpenXR which is what virtual reality headsets use. That makes sense because the display offers eye tracking and the sequential or side-by-side stereo methods would not be able to use the eye tracking to change the viewing angle as you moved your head, while software that uses OpenXR will allow that. ChimeraX can uses OpenXR, command "xr on". I did not see online what software you use with the display to work with OpenXR. It would need some SpatialLabs OpenXR display control software running on your computer. Here is a bit of discussion about trying to use this display with another 3D app called Slicer >> >> https://link.edgepilot.com/s/cad1c1c9/DC6RKYZmHE2WohxUaEbXfw?u=https://disc… >> >> where the poster did get Slicer's OpenXR to show 3D with the display. >> >> Let me know what you figure out. If you find some technical reference for the display online that explains the types of 3D input it accepts or how to set it up to work with applications that use OpenXR, I'd be interested in seeing that documentation. If it works well my lab might get a display. >> >> Tom >> >> >> >> >> On Oct 16, 2024, at 7:35 AM, Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> wrote: >> >> Hi Tom, >> I got a new 3d glasses free monitor. >> Acer 27" SpatialLabs View Pro Stereoscopic 3D Monitor - Black - FF.R2CAA.002 - Computer Monitors - CDW.com <https://link.edgepilot.com/s/f5cca637/LqUzzf13mUCbZBJiJkeIJQ?u=https://www.…> >> I used the spatiallabs (GO app) software to see stereoscopic 3d images from Chimerax, coot(mapfitting) amd MOE. Seemd to work fine. >> The Go app converts any 2d to 3d stereo when the program displaying is set to fullscreen. >> The Spatiallabs software from acer has plugins for unity , blender and a few other software suites. >> The Go app is compatible with *.obj and Gitf 3d formats. I tried those from chimerax and the result is spectacular. >> Is there any possibility of getting a chimerax plugin? >> Regards >> Krish >> >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Friday, July 12, 2024 1:22 PM >> To: Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> >> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> >> Subject: Re: [chimerax-users] 3d glasses free monitors from acer.... >> >> [EXTERNAL] >> >> Hi Krishnan, >> >> We do not have any of the new 3D laptops to try ChimeraX. Let us know if it works. You will probably use the ChimeraX command "camera stereo" to put it into 3D model on one of these 3D laptops. >> >> Samsung also showed a 3D monitor at January's Consumer Electronics Show with rumors that it may come out this summer. Also don't know if ChimeraX will work on that display. >> >> While I think ChimeraX stereo is likely to work on these displays a problem with past stereo that used shutter glasses was that only workstation graphics cards could do stereo in a window, meaning that part of the display is showing 3D (e.g. the ChimeraX graphics pane) while the rest is showing 2D. This required special graphics driver support only offered in the workstation cards (like Nvidia Quadro) and not in the consumer cards. Full screen stereo where everything is rendered in 3D was available on consumer cards mostly for video games where everything is in 3D including user interface elements. >> >> Let us know if you get something working. >> >> Tom >> >> >> >> >> >> On Jul 12, 2024, at 8:56 AM, Krishnan Raman via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> https://link.edgepilot.com/s/22d26e4a/CHuCkVzwKkGj1oPV_qX5bQ?u=https://www.… >> >> maybe we can see chimerax😊 in 3d in these… they do have a plugin for unity.. Iam trying get one of these to try things out. >> >> Krishnan Raman >> Executive Director, Structural Biology >> BioCryst Pharmaceuticals >> >> >> >> >> CONFIDENTIALITY NOTICE >> >> This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. >> >> _______________________________________________ >> 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://link.edgepilot.com/s/bb15c3bf/yEg7mgqw30m5lBrfcz6VNQ?u=https://mail… >> >> >> >> Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. >> >> >> >> CONFIDENTIALITY NOTICE >> >> This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. >> >> >> >> >> Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. >> >> >> >> CONFIDENTIALITY NOTICE >> >> This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. >> >> >> >> >> Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. >> >> >> >> CONFIDENTIALITY NOTICE >> >> This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. >> >

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Question about creation of splines for alpha helix models
by Shriya Sivakumar 18 Oct '24

18 Oct '24

Dear Sir/Madam, My name is Shriya and I am an undergraduate research assistant at the Microsystems and Mechanobiology Lab at Carnegie Mellon University. I was wondering if you could help me with regard to how ChimeraX creates splines when modeling alpha helices. In particular, which atoms from the protein backbone are used as the points through which the spline is calculated? Thank you! Sincerely, Shriya Sivakumar

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