April 2025 - ChimeraX-users - RBVI Mailing Lists

seeking help
by 张可依 20 Apr '25

20 Apr '25

Dear chimerax, hello, I would like to know if chimerax can draw protein secondary structure topology maps, and if so, can you tell me how to do the drawing?Something like the picture below Your help is of great importance to me and I, with my most sincere hope, look forward to your reply. All the best keyi [cid:494273c0-4f59-4f19-bd4d-5ac989d92136]

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Question about morphing trajectory
by Enrico Martinez 20 Apr '25

20 Apr '25

Dear ChimeraX users ! Using the following command, I generated a 200-frame trajectory that morphs through three selected conformations: morph #2,3,4 core 0.1 frames 200 wrap f rate linear Would it be possible to have the morphing trajectory end on the starting structure (so the full transition path ends on the first snapshot in the morphin trajectory), so that I can create a smoothly looped GIF animation? Many thanks in advance ! Enrico

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Combine PDBs in models instead of changing chainId ?
by Vincent CHAPTAL 18 Apr '25

18 Apr '25

Hi, using "combine #1-3" with 3 models having chain A only, it changes the chain Id to B and C for models #2-3, as described in the doc. Is it possible to combine PDBs as a multimodel PDB, seperated by MODEL keywords in the PDB file? Thank you. Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Request for Academic Use Confirmation Document – ChimeraX Demonstration Class
by Coordenação Farmácia_ 17 Apr '25

17 Apr '25

Dear UCSF ChimeraX Team, My name is Emanuell Santos, I am a pharmacist, Ph.D. in Drug Development Technology, and the coordinator of the Pharmacy program at a private Brazilian college. I also teach Medicinal Chemistry for both Pharmacy and Medical students. I am reaching out to respectfully request your support in including UCSF ChimeraX in a practical session of my Medicinal Chemistry course. The goal is to introduce students to molecular modeling approaches through a demonstrative class where they can also explore some of the software’s functionalities directly. This initiative is aligned with national educational guidelines from our Ministry of Education, which emphasize the inclusion of innovative and technological methodologies in undergraduate teaching. I plan to use the free academic version of ChimeraX solely for educational purposes and without any commercial intent. I kindly ask whether it would be possible to obtain a brief statement or document from UCSF (even if generic) confirming that such use falls within the allowed academic scope. This would be helpful in documenting compliance with institutional and governmental regulations. I greatly appreciate your attention and support, and I look forward to your response. Warm regards, Emanuell Santos Coordinator – Pharmacy Program FACENE/RN -- Prof. Dr. Emanuell dos Santos Silva *Coordenação de Farmácia - FACENE/RN* Por favor, confirmar o recebimento deste e-mail.

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Re: Unable to display GLY in Chimera
by Elaine Meng 15 Apr '25

15 Apr '25

Hello Qiang, I guess you are talking about ChimeraX, not Chimera. They are two different programs. You can just hide all the other glycine atoms. This is not a bug. The suppressBackboneDisplay *allows* you to show both cartoon and backbone atoms at the same time, but you can still hide all the atoms you don't want to show. cartoon suppress false hide :gly show :93 I hope this helps, 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 Apr 15, 2025, at 9:16 AM, Qiang Liu <liu01301(a)umn.edu> wrote: > > Hi Chimera > > I am a Chimera user and unable to display single GLY as stick and cartoon. I found commend "suppressBackboneDisplay", however this command makes all the GLYs displayed as stick and cartoon. I only want to display GLY93 as stick and cartoon and could you please let me know how to make it happen? Thank you. > > Qiang. > > -- > Qiang Liu, Aldrich Lab > Medicinal Chemistry, College of Pharmacy > University of Minnesota > > 8-115 Weaver-Densford Hall > 308 Harvard St SE > Minneapolis, MN 55455

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How to save the PAE plot as an image in ChimeraX using command line ?
by picasa1983＠gmail.com 14 Apr '25

14 Apr '25

Hi, I am using ChimeraX to visualize AlphaFold models and display the PAE plot with: alphafold pae #1 /path/to/confidences.json I would like to save only the PAE plot (not the 3D structure view) as a .png or .pdf file. What is the correct command to save the PAE plot image in ChimeraX? Thanks a lot!

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B-strand arrowheads
by Lee Bardwell 13 Apr '25

13 Apr '25

Hi Elaine and team, I’ve noticed an issue that sometimes happens when I change some residues to a beta strand, e.g. setattr /A:149-151 res ss_type 1. Sometimes an arrowhead is not placed at the end of the strand. Am I doing something wrong? Or is there a way to force an arrowhead? Thank you! _________________________________ Lee Bardwell, Ph.D. Professor and Vice-Chair, Dept. of Developmental & Cell Biology Charlie Dunlop School of Biological Sciences University of California, Irvine __________________________________

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Removing distance label from distance monitor
by Elaine Meng 13 Apr '25

13 Apr '25

> On Apr 12, 2025, at 2:01 AM, Yu GUO 郭宇 <guoyu60(a)westlake.edu.cn> wrote: > > Dear UCSF Chimera(X) team, > > I am using ChimeraX 1.9. As shown in the picture below, I labelled the atomic distance 1.52 A. I want to retain the dashed line but to remove the number "1.52". How can I realize this? > > Thank you! Next time, please send your questions to chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (CC'd here) --- if you send it to me only it may not get answered. I changed the subject line to describe the current topic. If you have distance monitors displayed there are several ways to hide the number labels. One way is command ~label pseudobonds If you just wanted to draw dashed lines and not show any distances, it may be a waste of time to use the "distance" command or Distances tool. Instead you can just use command "pbond" available in ChimeraX 1.8 or later, see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/pbond.html> I hope this helps, 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

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SwissDock dock4 in ChimeraX not recognized
by Nadia Elghobashi-Meinhardt 12 Apr '25

12 Apr '25

Dear all, When I try to open a SwissDock .dock4 file in ChimeraX, the swissdock format is not recognized. The chimeraX forum advises using "format swissdock" when opening the file, but I am getting 'invalid "format" argument'. Does anybody have a solution to this problem? Many thanks, Nadia -- Dr. Nadia Elghobashi-Meinhardt <https://people.ucd.ie/nadia.elghobashi-meinhardt> Assistant Professor (Ad Astra Fellow) School of Chemistry University College Dublin Belfield, Dublin 4, Ireland Tel: +353 1 716 2044

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Features of Chimera X
by Ogbuehi, Ulochukwu 09 Apr '25

09 Apr '25

Greetings, I had a couple questions about the usability of ChimeraX. 1. Is there a way I can insert a variant sequence, and it produce the structure that I would like modelled. Or would I have to strictly use a generated PDB file of my variant for ChimeraX to model the structure. 1. I was able to upload and model my WT protein structure in ChimeraX from the AlphaFold WT PDB file I downloaded; however, I am not able to generate a PDB file for my variants and would like to know if there is a feature that allows me to insert my aa sequence into ChimeraX to model the variant structure? Or maybe even a feature that allows you to generate a PDB file using an aa sequence. 1. Would I need the WT PDB file to be uploaded and modelled in ChimeraX first prior to adding in my aa sequence, granted that I am even able to insert an aa sequence directly into ChimeraX? Kindest Regards, Bethel Ogbuehi

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