- ChimeraX-users - RBVI Mailing Lists

How to remove a biological assembly from an atomic model
by Guillaume Gaullier 09 Oct '24

09 Oct '24

Hello, I am using the asymmetric unit of a PDB entry to define my own biological assembly based on a symmetric cryoEM map. Using the sym command, I can store the new biological assembly in the cif file. However, it seems I can't remove the biological assembly that came with the PDB entry's annotation, but that is now completely irrelevant because I moved the coordinates into my map (when I apply it, I get new chains completely outside the map). Is there a way to do this without needing to edit the cif file with a text editor? 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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Images in background
by Enrico Martinez 08 Oct '24

08 Oct '24

Dear ChimeraX Development Team, I would like to extend my appreciation for your continuous work on ChimeraX and the powerful capabilities it offers for molecular visualization. I previously inquired about the possibility of using static images as backgrounds, similar to what is available in UCSF Chimera. Together, we discovered a workaround by loading an image as a model, adjusting its orientation, and setting it as a static background. However, there is still a significant limitation: when rotating a molecular model (defined in a separate model), the entire scene—including the background—rotates. This compromises the visual experience, as it disrupts the intended static nature of the background image. I would like to formally request the introduction of a more robust solution that allows for the following: - The ability to set static images as true background elements that remain fixed when manipulating other models (e.g., rotating or zooming in on molecular structures). - Support for short background animations, allowing users to load video or animated files that can play while the molecular models are rotated and manipulated independently. These features would greatly enhance the flexibility and presentation capabilities of ChimeraX, making it easier to create high-quality visualizations and presentations. I believe many users would benefit from these enhancements. Thank you for considering this request, and I look forward to any updates on the possibility of implementing these features. Yours sincerely Enrico

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Buried SAS Area selection
by Fernando Villa 07 Oct '24

07 Oct '24

Dear Chimera users I have been trying to select the atoms involved in the interface of a receptor/ligand complex in ChimeraX without success. In UCSF Chimera e.g. open 4RSC del solvent sel #0:.b del sel select ligand zr>10 del sel focus measure buriedArea protein ligand sel @/buriedSASArea “Only atoms at the interface are selected” = OK **The interface buried area calculation was performed and the atoms involved in the buried area were selected. However, I wish to do the same in ChimeraX, for surface area calculations: e.g. open 4RSC del solvent del /B select ::name="A3V" view sel measure buriedarea protein withAtoms2 ligand sel t list t cutoff 0 “All atoms in the interface are selected per residue” = KO The results of the calculations are the following: UCSF Chimera = 719.643 ChimeraX = 719.65 = OK I have difficulties to select only the atoms in the interface, not all atoms of the residues, I have tried several ways to do this but it has been complicated, I even tried to insert the command “sel @/buriedSASArea” of UCSF Chimera in ChimeraX without success. Sincerely. Fer <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Libre de virus.www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Color Zone
by Mark Rosenberg 07 Oct '24

07 Oct '24

Using an atomic model and map, when I colour a different zone, I "lose" the colour from the previous zone I coloured. Is this a bug? This is in Windows 11. Thanks in advance.

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3MF Support
by Conrad Toms 07 Oct '24

07 Oct '24

Hello, Is .3MF export support planned for ChimeraX? It is overall a superior format to STL and has been seeing adoption in most programs for mesh work and 3D printing.

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Software copyright issue
by 姜恩誉 06 Oct '24

06 Oct '24

Hello, I would like to ask whether chimera software academic free includes the publication of papers? Looking forward to your reply, thank you 姜恩誉 2023111025(a)stu.njau.edu.cn

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Web server down?
by Roden Deng Luo 05 Oct '24

05 Oct '24

Dear ChimeraX Team, I am making a tutorial and notice that I cannot access the download page again. This is probably the fourth time I experienced this in recent months. Best, 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.

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Functionality request: Measure molecular weight
by Jan-Hannes Schaefer 04 Oct '24

04 Oct '24

Dear ChimeraX community, Thanks for your work and effort in making ChimeraX available to all of us. I would love to see a function in future versions of ChimeraX to measure the molecular weight of the model and link it to the uniprot entry? Let me know if this is something you would like to add. Yours, Jan ___________________________ Jan-Hannes Schäfer, PhD Lander Group • Scripps Research 10630 John J Hopkins Dr. San Diego, CA 92121 Mailing-code: TRY-21 jschaefer(a)scripps.edu (858) 784-8728

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Selecting a sidechain but not the cartoon backbone
by James Lingford 03 Oct '24

03 Oct '24

Dear ChimeraX team, I want to select only the sidechains of a protein in order to visually outline them for a figure. This isn't an issue if cartoons are turned off, because I can select the only sidechains I want and use the command: `sel sel & sidechain` and I outline them in a nice way with... `graphics sel col black width 2` However, if cartoons are turned on then this won't select just the sidechain, but select a portion of the cartoon backbone too. I'm not sure how to specify this. Ideally I want a transparent cartoon with opaque sidechains, and then have only the sidechains selected. Please see the images attached for examples of what I'm referring to. Many thanks, James [image: sidechain2.png] [image: sidechain1.png] -- *James Lingford* | Research Officer, Greening Lab Department of Microbiology, Monash Biomedicine Discovery Institute Monash University Google Scholar <https://scholar.google.com/citations?user=4KSRHTUAAAAJ&hl=en> | Website <https://www.jameslingford.com/>

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Coloring chains by attribute
by Juan Ortiz Mateu 02 Oct '24

02 Oct '24

Dear developers, I’m trying to color the ribosome (4ug0) with a color code for abundance of each chain (ribosomal proteins) found in my proteomics data. I have created an attribute successfully, as it says in the log: Summary of feedback from opening fc.defattr note Assigned attribute 'FC' to 32 chains using match mode: any However, in the Render/Select by attribute tool there is no option to color chains, only atoms/residues/structures. How can I apply these numeric values to color the different chains/subunits? Thank you, ******************************** Juan Ortiz Mateu Researcher PhD Student Membrane Proteins Lab Biotecmed Institute University of Valencia Dr. Moliner, 50 46100 Burjassot (Valencia) Spain research.uv.es/membrana/ **********************************

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