- ChimeraX-users - RBVI Mailing Lists

VR on ubuntu workstation
by arangarajan＠initialtx.com 24 Apr '25

24 Apr '25

Hi, i got steam VR installed but later found out that Oculus does not support linux. Is there a work around for using chimerax VR on latest ubuntu machine with oculus rift s headset? i can get other headset also if it will fit this purpose. thanks in advance, best amith

2 3

How can I overlay the 2Fo-Fc density map onto the amino acid residues I specified?
by 1025049892＠qq.com 24 Apr '25

24 Apr '25

Every time I open the map file in ChimeraX, I find that it doesn't overlap with my PDB structure. Why is this the case, and how can I make them match? Thank you for your attention. I'm looking forward to your reply.

3 2

Labeling chains in MD simulation trajectories of a multimer
by Alexandra Zahradnikova 24 Apr '25

24 Apr '25

Hi All, I am interested in MD simulations of homomultimeric ion channels, which I do in GROMACS. I would like to analyze my output files with ChimeraX but I run into the following problem: The .gro output of the simulation consists of a single chain named /? in ChimeraX. When I open the file in old Chimera, it shows every chain of the original protein separately but with the same name ()

3 6

Effect of clearing ChimeraX cache from Mac?
by Radford, Katelyn M. (Kate) 23 Apr '25

23 Apr '25

Hi there! I'm in the throes of a memory-expensive project and my computer is running out of space. A little bit of googling led me to conclude that it would probably make sense for me to clear my system's cache, as my system files take up about a third of my disk space. ChimeraX cache files account for a substantial portion of that memory usage. As I make figures, I save .cxs files of each figure so that it's easy to go back and edit things that need to be changed. My ChimeraX also has a bunch of plug-ins installed (e.g. ISOLDE). I'm wondering: how much damage will I do to my installation and to my .cxs files if I delete the ChimeraX cache? System and software details: ChimeraX version: 1.9 MacOS: Ventura 13.0 Chip: Apple M2 Max Thank you all so much for the excellent work you do, Best wishes, Kate Kate Radford (she/they) PhD candidate, Biochemistry and Molecular Biophysics California Institute of Technology 1200 E California Blvd Pasadena, CA 91125

3 2

Re: cartoon not displaying in ChimeraX despite complete backbone
by amith ranga 22 Apr '25

22 Apr '25

Dear ChimeraX users, I'm unable to display the cartoon representation for pdb file in ChimeraX, even though the residues and atoms appear complete. The structure contains standard RNA residues (A, G, U) , Each residue includes all expected backbone atoms (P, O5', C5', C4', C3', O3', C1', O4', etc.) as well as complete base atoms and hydrogens. The file was written out from MOE software and I am not sure if this is an issue. Some tips on how to edit the pdb file would be helpful Thanks, amith

4 3

[ISOLDE] Handling Lys-Asp iso-peptide bonds and D-amino acids
by Yang Lee 22 Apr '25

22 Apr '25

Addressing this to Tristan, in all likelihood. Is there a way of parameterising KD isopeptide bonds and D-amino acids? Perhaps a secret three letter code I can rename the residues to make them play nice? Unfortunately, I'm trying to model a peptide that has both of these exotic elements. Cheers, Yang

3 15

Color of unrolled density maps
by Sen, Anindito 21 Apr '25

21 Apr '25

Dear ChimeraX Team, Is there a way we can keep/restore the color of the unrolled helical density maps ? Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu<http://microscopy.tamu.edu/>

2 1

Re: Regarding peptide bond formation using chimeraX
by Tom Goddard 21 Apr '25

21 Apr '25

Hi Harpreet, I'm not sure how you deleted the bond. If you deleted a peptide bond with delete bonds /A:102@C /A:103@N or the equivalent menu Actions / Atoms and Bonds / delete then you could just recreate it with bond /A:102@C /A:103@N I'm not sure why you would do that since there is no need to delete a bond to move the two pieces of the structure. Instead maybe you split the protein into two separate models. In that case you can't simply add a bond between different models, instead you have to combine the models (e.g. command "combine #1,2"). You might get better answers on the ChimeraX mailing list, so I have CC'ed that list. Tom > On Apr 21, 2025, at 4:06 PM, Singh, Harpreet <harpreet.singh2(a)ucsf.edu> wrote: > > Dear Professor Goddard, > > I hope you are doing well. > > I am a Postdoctoral scholar from the Robert M. Stroud lab. I recently deleted a peptide bond from our protein structure to adjust the model for cryo-electron microscopy (cryo-EM) mapping. I am now attempting to reconstruct the peptide bond using the Build Structure tool. However, I am encountering an error message indicating that there are no chain-terminal carbons in the atoms. > > I would appreciate your assistance in resolving this issue. > > Thank you for your time and consideration. > > Best regards, > Harpreet Singh > Postdoctoral Fellow, Stroud lab > Department of Biochemistry and Biophysics > UCSF

1 0

Color of unrolled density maps
by Eric Pettersen 21 Apr '25

21 Apr '25

The original was sent to the wrong address (chimerax-users-bounces)… Dear ChimeraX Team, Is there a way we can keep/restore the color of the unrolled helical density maps ? Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu <http://microscopy.tamu.edu/>

1 0

Quality of sphere representation
by Enrico Martinez 21 Apr '25

21 Apr '25

Dear ChimeraX users! I wonder if there is a special option which would allow me to increase the quality of sphere representation (which are displayed by default for big cryo-em protein complexes loaded in chimeraX) in the same way as it can be done for surfaces using gridSpacing ? Many thanks in advance Enrico

2 1

Concatenating trajectories in ChimeraX
by Alexandra Zahradnikova 20 Apr '25

20 Apr '25

Dear All, I am new in molecular simulation and not very much experienced with ChimeraX. I did not find an easy way to concatenate trajectories (in my case, .xtc files from gromacs). Any suggestions would be welcome. Thanks in advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796

4 4

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]

2 1

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

2 3

Combine PDBs in models instead of changing chainId ?
by Vincent CHAPTAL 17 Apr '25

17 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/

2 2

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.

2 2

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

1 0

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!

4 5

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 __________________________________

2 1

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

1 0

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

2 2

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

2 1

Refinement in ISOLDE failing
by Firdous Tarique 09 Apr '25

09 Apr '25

Dear everyone I am trying to refine my protein using ISOLDE in ChimeraX which is failing with the following error. "At least one residue in your model does not match any templates in the MD forcefield. This may be due to missing or superfluous atoms, or an unusual residue that has not yet been parameterised. Launching the unparameterised residue widget to help sort this out." The protein contains two heme molecules and Ca ions which obviously is the reason why it is failing. Once these molecules are deleted it runs fine. My question is how to add that specific MD force field for these molecules in order to run the ISOLDE in ChimeraX. Any input would be appreciated. Firdous

1 1

Re: issues with writing models as pdb files
by arangarajan＠initialtx.com 08 Apr '25

08 Apr '25

Hi everyone, I noticed that sometimes when i write pdb of one model or a selection , it does not open in other programs.( MOE,Pymol). One of the errors i noticed recently was that th pdb file was written as a multi model pdb file ( each of the 70 residues in the protein were separate models) , i cleaned it using notepad++ by removing the model lines and it was opening correctly. i was told that it might be related to using split command. i use split often and it might be the case. can some one please explain how using split can lead to this? and if so what is best way to fix it? should i perhaps run some version of combine command on the model prior to writing it out as pdb file. thanks again, best amith

3 4

Issues with find cavities tool
by Marino, Claudia 08 Apr '25

08 Apr '25

Greetings, I am not sure why I recently cannot longer use the tool “find cavities”. My ChimeraX version is 1.9 and my MacOS is Sequoia 15.4. Please, find below the screenshot of the Error message. [cid:image001.png@01DBA7F0.57B85750] Thank you very much in advance for your help. Sincerely, Claudia.

3 7

Can't open ChimeraX on my Win11
by kangkang042＠126.com 07 Apr '25

07 Apr '25

About 2 weeks ago, it worked fine. Today when I click the ChimeraX startup, nothing happened. I reinstalled the lastest version v1.9, nothing changed. Run ChimeraX-console.exe in cmd, it shows these information: NOTE: Traceback (most recent call last): File "<frozen runpy>", line 198, in _run_module_as_main File "<frozen runpy>", line 88, in _run_code File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\core\\__main__.py", line 1217, in <module> exit_code = init(sys.argv) ^^^^^^^^^^^^^^ File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\core\\__main__.py", line 653, in init sess = session.Session( ^^^^^^^^^^^^^^^^ File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\core\session.py", line 551, in __init__ from chimerax.graphics.gsession import register_graphics_session_save File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\graphics\\__init__.py", line 37, in <module> import chimerax.arrays File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\arrays\\__init__.py", line 24, in <module> from ._pyarrays import get_lib, get_include, load_libarrays File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\arrays\\_pyarrays.py", line 40, in <module> from . import _arrays ImportError: DLL load failed while importing _arrays: 找不到指定的模块。 BUG: ImportError: DLL load failed while importing _arrays: 找不到指定的模块。 File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\arrays\\_pyarrays.py", line 40, in from . import _arrays _See log for complete Python traceback._ My PC: Win11 Pro Workstation 26100.3624

2 3

How to browse inspect ligands?
by Guillaume Gaullier 04 Apr '25

04 Apr '25

Hello ChimeraX team, These days I look a lot a structures of photosystems, which contain large numbers of ligands: chlorophylls, carotenoids, etc. each by the dozens, adding up easily to more than 100 ligands. Is there any tool to browse through all ligands systematically? Ideally something similar to the sequence viewer, but for ligands. Or a way to generate a list with chain IDs and "residue" numbers reported, and clicking rows in the list would select the corresponding ligand. I looked for something like this, but couldn't find anything. Thank you in advance, 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

4 5

saving cloned structures on chimerax inquiry
by Joel Gallardo 03 Apr '25

03 Apr '25

to whom it may concern, i have mapped out a mol2file onto a structure found in a .mrc file. and then i ran this command to multiply the mol2 structure: sym #2 h,0.357979,132.83196,72,-40 coord #1 center 119.04,119.04,119.04 it multiplied it as intended which is good but now i want to save those multiplied mol2 files into a sperate mol2 files. i tried this command: save multiplied_structures.mol2 format mol2 models #2 but this only saves a single mol2 structure into the new mol2 file. i want all 72 molecules in one mol2 file. can you give me some advice as to how i may be able to do this? my ultimate goal is to take that mol2 file and do an md simulation. Best, Joel Gallardo (Graduate student in chemistry)

2 3

Keeping track of H-bonds in trajectories
by Alexandra Zahradnikova 02 Apr '25

02 Apr '25

Hello, I am new in molecular simulation and not very much experienced with ChimeraX. Is there a way to keep track of H-bonds between two specific residues (they can form one or more H-bonds) during the course of the trajectories (in my case, .xtc files from gromacs)? Thanks in advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796

2 2

Model loops with MODELER in ChimeraX
by Alexandra Zahradnikova 02 Apr '25

02 Apr '25

Hello, I have recently watched a Youtube video (https://www.youtube.com/watch?v=GV6jHhxR5T4) about completing loops with Modeller in ChimeraX. However, the structure I want to model is only a part of the actual molecule, and I want to replace one unresolved segment (300 residues long) with 11 glycines. When I upload both, the FASTA file with the sequence as it should look after completion of the loops, and the PDB file of the incomplete structure, I am not able to align them together in order to perform the modelling. - If I use the original PDB file containing the SEQRES part, the association is performed but produces mismatches after the start of the unresolved sequence. - If I use the PDB file without the SEQRES part, I am not able to perform the association. Can anybody help me? Thanks in advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796

3 2

Create new attributes
by javisanchezdelrio＠gmail.com 31 Mar '25

31 Mar '25

Hello! I am trying to create a new attribute in a cif file called align_rmsd. For the example, assume I want all atoms to have this attribute equal to 5. For this, I am opening the file in ChimeraX and applying the following command: setattr atoms align_rmsd 5.0 create true type float With the following result: Assigning align_rmsd attribute to 145 items However, when I do "save new.cif" I don't see any new attribute in the loop _atom_site.align_rmsd nor any value equal to 5. How can I store this values in a new cif file so that I see the values equal to 5? Thank you in advance! Javier

3 2

Downloading ISOLDE
by Ashley Gutierrez 28 Mar '25

28 Mar '25

Hi there, I am having a bit trouble downloading the ISOLDE bundle. While I can download the .whl to my computer, it will not open in ChimeraX. Please let me know if I am missing some commands in between, I am new to this system. Thank you (:

2 1

Ligand flying movie in chimeraX
by Matzov Donna 26 Mar '25

26 Mar '25

Hello, I'm trying to create a movie in Chimerax similar to the "Ligand flying into unbound conformation" that was in the old Chimera movie tutorials (https://www.cgl.ucsf.edu/chimera/data/tutorials/movies08/moviemaking.html) I tried using the "reset" command, but it seems like it doesn't exist in ChimeraX. Is there a command that replaces it? Alternatively, I would be happy for any suggestion for how to get an effect similar to the flying ligand in ChimeraX. Thanks, Donna Donna Matzov, PhD Department of Structural Biology Weizmann Institute of Science The Shalev-Benami Lab<https://www.weizmann.ac.il/Structural_Biology/Shalev-Benami/home>

2 2

Change location of .cache/ChimeraX ?
by James Vincent 24 Mar '25

24 Mar '25

Hello ChimeraX Devs/Users, Is there a way to specify the location of the .cache/ChimeraX directory? As far as I can tell it is always $HOME/.cache/ChimeraX (on Linux machines). I see no options or configs to change this. We are installing ChimeraX on a multiuser system and would like to add a plugin/ bundle to be available for all users ( ChimeraX_ScipionExtensions 1.3). Perhaps I missed this in the documentation, but is there a standard way to add plugins so that they are available for all users? Thanks, Jim

2 1

Force display of helix with setattr
by Kevin M Jude 24 Mar '25

24 Mar '25

For some reason the selected residues in this image are not displayed as a helix in ChimeraX. I think the command to force it woud be ‘setattr sel res ss_type 1’, but nothing changes (the log says “Assigning ss_type attribute to 2 items”). Same result if I try ‘setattr sel res is_helix 1’. Can anybody please set me straight (and my cartoons helical)? Using ChimeraX 1.9 for OS X. Thanks for any help. [cid:image001.png@01DB9CD2.E2CD6B60] -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305

2 2

Inactivate models
by Burgers, Peter 24 Mar '25

24 Mar '25

Dear team, Classic Chimera had a command to turn off specific models, allowing manipulation of the other model(s). What is the command for that in ChimeraX? ChatGPT gave as answer “model toggle off #1” but that appears to be wrong. Thank you, Peter ---------------------------------- Peter M.J. Burgers Marvin Brennecke Professor of Biological Chemistry Department of Biochemistry and Molecular Biophysics Washington University School of Medicine BOX 8231 660 South Euclid Saint Louis, MO 63110 E-Mail: burgers(a)wustl.edu<applewebdata://1B940EF6-0122-4328-902B-DCB358A99492/burgers@biochem.wustl.edu> PH (314) 362-3872 (office) 286-2554 (lab) FAX (314) 362-7183 http://biochem.wustl.edu/~burgersw3/ ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

2 5

Problem with setting up Modeller
by Miloslav Radoslavov 24 Mar '25

24 Mar '25

Greetings, I encountered an issue when attempting to utilize the "Model Loops" option. After installing Modeller and specifying the path to it, Chimera X did not prompt me to input my activation key. Instead, it indicated that no Modeller key was provided. Also the console command "modeller licenseKey ...." does not seem to work. Could someone please assist me in resolving this issue? Is there an alternative method to input my key? Thank you in advance, M. Radoslavov

2 1

Error using matchmaker
by javisanchezdelrio＠gmail.com 23 Mar '25

23 Mar '25

Hello, I am trying to use matchmaker command (matchmaker #1 to #2 showAlignment true) with two cif files I've obtained from Kihara and Modelangelo. The problem is that, once I try to use the matchmaker command, I obtain the following error: "No matrix compatible with both reference structure and all match structures" and I don't know what is failing. Is it because the two structures are too different from each other? I hope I can get more information about this error message Thank you in advance, Javier

4 5

ChimeraX 1.9 dark theme
by jinlun_kylian zhang 22 Mar '25

22 Mar '25

Hi chimeraX developers, I've used chimeraX for a long time and today I upgraded it to 1.9, But i can't help to notice the chimeraX's theme has been set to dark rather light/white theme in 1.8. Can you please assist me to modify this dark theme back to white? I am more used to that. [image: image.png] Best, kylian

2 1

Switch Dark theme of chimeraX1.9 back to white theme
by hytxnt123＠gmail.com 22 Mar '25

22 Mar '25

Hi, I just upgrade my chimeraX to v1.9 but I dont really fit in the dark theme. Can anyone help me to switch back to the white theme just like v1.8?

2 1

Advice on Meeting settings
by Edwin Kyi 20 Mar '25

20 Mar '25

Hello, We have been experimenting with the Meeting command in VR and are seeing some real uses for guided teaching sessions. We're looking for ways to finesse set up for these sessions and I wonder if you could help with some technical questions we have: 1. What main optimisations of the settings would you recommend for smoother running in VR? 2. Is there an easy way to toggle off all people's interactions with the model with one command except the host? 3. Same as Q2, is there an easier way to toggle off people's hands unless they are the ones asking a question? 4. Can the VR ava VR be resized ie. smaller? Kind regards Edd Edwin Kyi Multimedia Learning Experiences Developer (CTL) Join the VR Society, see: https://www.guildofstudents.com/organisation/ubvr/ +44 121 415 9049 University of Birmingham Collaborative Teaching Laboratory (CTL) Edgbaston Birmingham B15 2TT www.birmingham.ac.uk<http://www.birmingham.ac.uk/> Twitter<https://twitter.com/unibirmingham> / Instagram<https://www.instagram.com/unibirmingham/> / Facebook<https://www.facebook.com/unibirmingham> / LinkedIn<https://www.linkedin.com/school/university-of-birmingham/> [University of Birmingham logo.]<https://www.birmingham.ac.uk/index.aspx> For the most up-to-date-information, visit: www.birmingham.ac.uk<http://www.birmingham.ac.uk/>

3 2

ChimeraX not communicating with GPU
by #TAN YONG JUN EDDIE# 20 Mar '25

20 Mar '25

Dear Developers, Hope this email finds you well. I have encounter an issue regarding the GPU driver usage for chimeraX. The issue is that the model and density movement is very choppy at step size 1, with a box size of 400. Here are some information on the software that I am using. Downloaded Software: Ubuntu 22.04 (Linux) ucsf-chimerax_1.9ubuntu22.04_amd64.deb<https://www.cgl.ucsf.edu/chimerax/cgi-bin/secure/chimerax-get.py?file=1.9/u…> This is my current nvidia driver and cuda version: NVIDIA-SMI 560.35.05 Driver Version: 560.35.05 CUDA Version: 12.6 It came to my attention that it is not utilising GPU upon running "graphics driver" on chimeraX, which outputs: graphics driver OpenGL version: 4.5 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.3 OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits) OpenGL vendor: Mesa additionally, it is not showing up under nvidia-smi when I am running the program. Is there any solutions to this issue? Thank you in advance. Regards, Eddie

2 1

Protein-Protein Interaction Prediction
by Charity Conlin 19 Mar '25

19 Mar '25

Hello, I am trying to use ChimeraX to predict the interaction of 2 proteins using alphafold: Beta-Lactoglobulin and Lactoferrin. I have plugged the 2 protein sequences into the alphafold tool to try to predict the interaction, but I get a failure code in google colab. I am wondering how I can get around this? I think it is because the wrong versions of numpy and colab are installed during the program. Thanks, Charity [cid:b73a7660-3878-48cf-87d5-ddcd6ab388c2]

2 4

Poor performance on Ubuntu w/ discrete graphics vs basic b laptop
by ben 19 Mar '25

19 Mar '25

I'm looking for trouble shooting tips on poor graphics performance on linux. I have read through the FAQ's and done a basic search of the chimera list. Observed: Symptom: Prohibitively slow rendering when just rotating a map, especially if a model is loaded as well. When using Isolde (and presumably anything with clipper) performance is more "normal" as only a small portion of the map is displayed. System: This is observed on Ubuntu distros (both 20.04 22.04) with their respective Chimerax packages, tested versions 1.6.1 and 1.9. Nvidia drivers installed via the cuda toolkit (535.183.01 CUDA Version: 12.2 ) GPUs are either rtx 3090 or 4090s Point of reference: Performance is compared to my relatively very underpowered Windows thinkpad w/o discreet graphics. Thanks for any pointers to resources! Ben Sent with [Proton Mail](https://proton.me/mail/home) secure email.

2 3

Issue with crashing after mac upgrade to Sequoia
by Lee, Juliet A. 19 Mar '25

19 Mar '25

Hello! I recently updated my Mac (M2) to Sequoia 15.3.2, and I have had a specific issue in ChimeraX since then (though I cannot be 100% positive the two things are linked). Basically - whenever I try to save (anything) in ChimeraX, the application stops responding and I have to quit it. I downloaded the newest version 1.9 of ChimeraX as well as the daily build version - but this problem persists. I read about issues with the graphics driver - but these seem to be limited to Intel chips... Hoping you might have some insight as to why this is occurring, thank you!!! Sincerely, Juliet

3 7

secondary structures
by Bajaj, Ruchika 18 Mar '25

18 Mar '25

Hi I want to determine helices and betasheet and their ranges in a structure. Could you please let me know which command and its usage I can use to get it. Please let me know. Thanks !! Regards Ruchika

2 2

Request for Review of Figure 12 instructions
by Zeenat Bashir 18 Mar '25

18 Mar '25

Dear ChimeraX Developers, I hope this email finds you well! I am developing a hands-on module for students using ChimeraX, and I want to express my appreciation for this powerful and beautifully designed tool. I would like to request a review of the instructions on page 11 for generating Figure 12. I have successfully generated this figure before and am now attempting to do so using ChimeraX. However, I would appreciate your guidance to ensure the accuracy and clarity of the instructions (I have highlighted it in red) Thank you for your time and support! I look forward to your feedback. Best Regards, Zeenat -- *Dr. Zeenat Bashir* *Senior Lecturer* *Biotechnology Lab Coordinator* *Department of Chemical and Biomolecular Engineering* *University of Pennsylvania* *310 Towne Building* *220 S. 33rd Street* *Philadelphia, 19104 -6393* bashirz(a)seas.upenn.edu

1 1

sybyl vs amber atom types in ChimeraX
by laurene.jacquot 17 Mar '25

17 Mar '25

Dear ChimeraX community, I hope this message finds you well. I am a master student currently working on a project where I need to generate a mol2 file with amber atom types for a protein. Chimera does not manage to parametrize my protein at all, which is why I switched to ChimeraX. ChimeraX does manage to generate a mol2 file, but it writes sybyl atom types. Despite looking on forums, I have not found a feature like in Chimera to write amber atom types instead. I was wondering if such a feature exists in ChimeraX ? Thanks in advance, Best, Laurène Jacquot PSL University, ChimieParisTech

4 3

Automating the process of data generation via ChimeraX
by mishra.ananya.163＠gmail.com 17 Mar '25

17 Mar '25

Dear Sir/Madam, I am an undergraduate student working on a project and I am trying to generate values for the solvent accessible surface area, mean molecular lipophilicity potential and mean surface electrostatic potential for a dataset involving protein 3D structures (in pdb format). We also plan to introduce point mutations via ChimeraX using the swapaa command and measure the same values for the mutated proteins. As such, we were wondering if there is a way to automate this process of generating the values for each protein, without having to manually do it. We tried to test out some code to see if it is possible to run a python file in ChimeraX. This was the code we wrote: import chimerax import csv import os from chimerax.core.commands import run run(session, "open" + r'C:\Users\anany\Downloads\Research\Test_PDB_Passenger\P35579_MYH9.pdb') run(session, "color red") run("surf") However, we received this error message: openC:\Users\anany\Downloads\Research\Test_PDB_Passenger\P35579_MYH9.pdb Traceback (most recent call last): File "C:\Users\anany\Downloads\Research\Test_PDB_Passenger\test_import.py", line 6, in <module> run(session, "open" + r'C:\Users\anany\Downloads\Research\Test_PDB_Passenger\P35579_MYH9.pdb') File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3156, in run raise UserError(self._error) chimerax.core.errors.UserError: Unknown command: openC:\Users\anany\Downloads\Research\Test_PDB_Passenger\P35579_MYH9.pdb Error opening python file C:\Users\anany\Downloads\Research\Test_PDB_Passenger\test_import.py We would appreciate your kind assistance! Thank you!

4 6

Feature request alphafold: return selection when dragging in PAE plot
by Vorländer,Matthias Kopano 17 Mar '25

17 Mar '25

Dear ChimeraX team, I love the alphafold tools in ChimeraX, and have a small suggestion to make it even better. Currently, when associating a PAE plot from a JSON file, you can drag the mouse in the PAE plot to color the corresponding residues (magenta and lime), but the residues do not become selected (although the color command gets printed in the log). I think it would be helpful if there was an option (or default behavior) to return a selection in addition, so that the selected region could be saved as a named selection, the display style changed ect… Or am I missing anything? Many thanks in advance, Matthias

2 1

Fwd: Re: coloring surfaces by electrostatic potential from different atoms
by Boaz Shaanan 16 Mar '25

16 Mar '25

Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel ---------- Forwarded message ---------- From: Boaz Shaanan <bshaanan(a)bgu.ac.il> Date: Mar 16, 2025 18:32 Subject: Re: coloring surfaces by electrostatic potential from different atoms To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Cc: Hi Elaine, Thank you so much for the prompt an informative reply. The points about the offset and dielectric are very relevant. In fact, in a quick test that I ran before posing the question I noticed that the coloring of the electrostatic potential on the cofactor was quie dim, probably because of those parameters. I'll also look into the MOLE and pseudo atom coloring. Thanks again. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Mar 16, 2025 17:50, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: Hi Boaz, I changed the subject line to try to describe this topic. We aren't the APBS experts but my understanding is that yes, it will generate potential at all points in the rectangular grid, based on the input atoms charges and locations. There will of course be potential values even at grid points where there are no atoms, since electrostatics are fairly long-range interactions. However, the magnitude will depend on what dielectric parameters you have given the calculation. Whether it makes sense: that is somewhat up to your scientific judgement. In my opinion, yes, it makes sense, but you have to think carefully about the "offset" you use to color the cofactor surface. Normally when the surface is on the same atoms that produced the charge, you use a positive offset (default 1.4) to color by values projected that distance outward from the surface, to represent what other outside atoms might "see". If you are coloring a surface of the cofactor atoms to try to understand the potential from the protein that the cofactor "sees," you should consider instead using a negative (say -1.4) or zero offset. The offset is adjustable in the Surface Color dialog options and the "color electrostatic" command: <https://protect.checkpoint.com/v2/r02/___https://rbvi.ucsf.edu/chimerax/doc…> <https://protect.checkpoint.com/v2/r02/___https://rbvi.ucsf.edu/chimerax/doc…> Note that an analogous procedure could be done in ChimeraX with the Coulombic electrostatic potential. For example, see the MOLE channels tutorial where we calculate the Coulombic potential from the protein but then show a surface on pseudoatoms representing a channel calculated by MOLEonline, and then color that channel surface by the protein potential. <https://protect.checkpoint.com/v2/r02/___https://www.rbvi.ucsf.edu/chimerax…> 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 Mar 15, 2025, at 10:30 AM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi friends, > On a related issue: > I'd like to explore the effect of replacing Val by Asp on the electrostatic potential 'seen' by a cofactor which is completely surrounded by the protein (this is relevant for understanding the change in reaction rate following such replacement). I thought of the following steps: > > • Omit the cofactor from the pdb2pqr and APBS. > • Read into chimerax the complete pdb (i.e. including the cofactor). > • Generate the surfaces (protein and cofactor). > • Render the electrostatic potential on both surfaces (i.e. Cofactor and protein surrounding it) and probe the potential on the cofactor. > • Does it make sense? Does APBS generate potential values in the void where the cofactor resides even though it wasn't present in the input pdb2pqr (i.e. in the void where the cofactor resides). > I'd appreciate your input. > Boaz >

1 0