October 2024 - ChimeraX-users - RBVI Mailing Lists

Configuring ChimeraX AlphaFold “Fetch” and “Search” features
by Jim Thorpe 10 Oct '24

10 Oct '24

Hi ChimeraX Team In our commercial lab we are unable to access public domain AlphaFold databases, and instead have our own copy on-premises. Is there a mechanism to reconfigure the ChimeraX AlphaFold “Fetch” and “Search” features to query our in-house copy? ChimeraX error reported is: Fetching url https://alphafold.ebi.ac.uk/files/AF-Q5STB3-F1-model_v4.cif failed: HTTP Error 403: Forbidden Many Thanks for advising me Best Regards Jim [cid:image001.png@01DB1A36.151649E0] Jim Thorpe Scientific Investigator Protein, Cellular & Structural Sciences Target Discovery GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK james.h.thorpe(a)gsk.com [cid:image002.png@01DB1A36.151649E0]<https://www.gsk.com/> [cid:image003.png@01DB1A36.151649E0]<https://www.facebook.com/GSK> [cid:image004.png@01DB1A36.151649E0]<https://twitter.com/GSK> [cid:image005.png@01DB1A36.151649E0]<https://www.linkedin.com/company/glaxosmithkline> GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information. GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation.

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Changing dihedral angle
by Prathvi Singh 09 Oct '24

09 Oct '24

Hi Elaine, Is it possible to change the dihedral angle between any given four sets of atoms, say CA,CB,CG, HG2 of a Lysine residue using command line in either chimera/chmeraX? Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Re: [Chimera-users] Center and Orient
by Tom Goddard 09 Oct '24

09 Oct '24

The documentation explains how to measure symmetry for a helical map https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#symmetry You have to use the helix option to give it some clue about the rise and twist angle per asymmetric unit step. Tom > On Oct 9, 2024, at 2:41 PM, Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> wrote: > > I need to explicitly give the symmetry (helical) because the command > > > measure symmetry #1 set true (#1 is my map) > > reports: > > No symmetry found for my_map.mrc > > > H. > > > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Wednesday, October 9, 2024 12:32 PM > To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu <mailto:hernando.sosa@einsteinmed.edu>> > Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> List <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> > Subject: Re: [Chimera-users] Center and Orient > > CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. > Hi Hernando, > > Here is how to apply symmetry to one copy of an atomic model in a symmetric cryoEM map in ChimeraX. First use the "measure symmetry" command to determine the map symmetry, then use the "sym" command to make the symmetric copies of the atomic model. Here is an example > > open 8ofx > open 16862 from emdb > measure symmetry #2 set true > sym #1 symmetry #2 > > Tom > > > On Oct 9, 2024, at 7:52 AM, Hernando J Sosa via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thanks Elaine, > > I will try to do this with ChimeraX. What I am trying to to do is to generate symetry related copies of a model fitted into a density map using the sym command. I noticed that the only way to define the center of symetry to be centered on the density volume was using the option center #n (where n is the id of the voume density) but only after doing center and orient by pressing the buttons in the volume viewer. > > Although chimeraX is much more prowerful I still find hard to find the the equivalent in ChimeraX of some operations that I use often in Chimera. 😉 > > Thanks again, > > Best > > H. > > _ > From: Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> > Sent: Tuesday, October 8, 2024 5:04 PM > To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu <mailto:hernando.sosa@einsteinmed.edu>> > Cc: chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> > Subject: Re: [Chimera-users] Center and Orient > > CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. > > In Chimera, there may not be commands that do exactly the same thing as some button. You might look at "focus <model-number>" and "reset" (maybe only if one model is open, or they haven't been moved relative to one another?) but in my tests, they did not do exactly the same thing as those buttons. > > That's one reason ChimeraX is way better than Chimera! You can use the GUI and it shows the command that it used in the Log. > > Best, > 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 Oct 8, 2024, at 1:38 PM, Hernando J Sosa via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: > > > > Dear Chimera, > > > > What would be the equivalent commands to the Center and Orient buttons at the bottom of the Volume Viewer menu tab? > > > > Thanks > > > > H. > > _______________________________________________ > 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/

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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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