March 2025 - ChimeraX-users - RBVI Mailing Lists

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 11 Mar '25

11 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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