February 2024 - ChimeraX-users - RBVI Mailing Lists

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

21 Feb '24

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

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

21 Feb '24

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

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Image as the background
by Enrico Martinez 21 Feb '24

21 Feb '24

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

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

20 Feb '24

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

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

20 Feb '24

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

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

19 Feb '24

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

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Surface color by homology
by Pedro Bule 17 Feb '24

17 Feb '24

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

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

16 Feb '24

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

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Swissdock
by Gabriel López Velázquez 14 Feb '24

14 Feb '24

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

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Size of side chains
by Binh Nguyen 14 Feb '24

14 Feb '24

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

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