- ChimeraX-users - RBVI Mailing Lists

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

20 Feb '24

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

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

20 Feb '24

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

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

19 Feb '24

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

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Surface color by homology
by Pedro Bule 17 Feb '24

17 Feb '24

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

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

16 Feb '24

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

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Swissdock
by Gabriel López Velázquez 14 Feb '24

14 Feb '24

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

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Size of side chains
by Binh Nguyen 14 Feb '24

14 Feb '24

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

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

14 Feb '24

Hello chimerax-users, I recently started using ChimeraX in more custom ways for specific analyses, for which I need several tools displayed at once. I need some docked and others floating. So the "Save tool position" option is very helpful. However, it saves window size only for floating tools, not docked ones, so I have to resize the docked tools at every restart (their position is saved correctly, but not their size relative to the main ChimeraX window). This happens for the model panel and log, that I have docked to the right of the 3D display: they systematically start much wider than I want (and than I resized them to last time I started ChimeraX). This doesn't happen for a custom button panel that I have docked to the right of the toolbar (but maybe because the command file generating the panel sets a fixed size explicitly?). I have not checked whether this happens with other tools. Is this normal behavior? If so, is there any way I can make docked tools remember not only their position but also their size? A quick search in the documentation didn't answer this question. Thank you, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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

12 Feb '24

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

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Chimera Script
by Dixson, Jamie 12 Feb '24

12 Feb '24

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

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