- ChimeraX-users - RBVI Mailing Lists

Boltz-2
by Lynne Howell 09 Jun '25

09 Jun '25

I’m sure it already on your radar – but would love to see Boltz-2 and its ability to predict binding affinity integrated into ChimeraX – as you did for Boltz-1. Thanks L P. Lynne Howell Canada Research Chair (2006-2020) Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children Professor, Department of Biochemistry, University of Toronto Office and Mailing address: Room 20-9-715 Peter Gilgan Centre for Research and Learning (PGCRL) 686 Bay St. Toronto ON M5G 0A4 Phone: 416-813-5378 (Internal 305378) Web page: https://lab.research.sickkids.ca/howell/ ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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Re: Robust way to setup scene and save image such that zoom and resolution are always the same across different monitors
by Daniel Larsson 09 Jun '25

09 Jun '25

I think what throws you off is the aspect ratio of the ChimeraX window. Add a command to set the size of the window into your workflow. For example: windowsize 800 800 Regards, Daniel From: Samuel Haysom via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> Reply to: Samuel Haysom <Samuel.Haysom(a)Nxera.life> Date: Monday, 9 June 2025 at 17:10 To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] Robust way to setup scene and save image such that zoom and resolution are always the same across different monitors Hello, Is there a recommended set of commands to setup a particular view of a molecule and then save an image of that view such that the size of the molecule within the image, the resolution of the image, and the position of the clipping planes will always be the same regardless of what monitor size/resolution it is taken on? Currently I setup an image using the following commands: e.g. view matrix camera 0.98237,-0.066404,-0.17474,86.421,0.014131,-0.90572,0.42363,190.37,-0.1864,-0.41863,-0.88882,-48.082 clip near -10 far 10 position /R:LIG zoom pixel 0.0348 I then save it using: e.g. save 'dir_path/image.png' width 2000 height 2000 supersample 10 transparentBackground False I often will come back to the same cxc script and want to re-render with e.g. a modified pdb file but still want to get exactly the same view. I can then substitute this picture into a figure I've created in e.g. Inkscape without having to resize the image. However I've noticed that often the new image will not have the same zoom (so the model will be bigger and smaller within the total FOV) which means I have to then manually resize it to match what I already have. I've also noticed that if I render on e.g. my laptop rather than my desktop monitors this effects both the zoom as previously mentioned but also the final resolution of the image as this seems tied to the screen resolution. Is there a way to make it so the image will always look the same regardless of hardware etc.? KR, Sam Samuel Haysom<mailto:Samuel.Haysom@nxera.life> Senior Scientist • Protein Sciences Nxera Pharma UK<https://nxera.life/> Limited +44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom [cid:image001.png@01DBD963.DEF37B10] The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Nxera Pharma UK Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989. VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ 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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Robust way to setup scene and save image such that zoom and resolution are always the same across different monitors
by Samuel Haysom 09 Jun '25

09 Jun '25

Hello, Is there a recommended set of commands to setup a particular view of a molecule and then save an image of that view such that the size of the molecule within the image, the resolution of the image, and the position of the clipping planes will always be the same regardless of what monitor size/resolution it is taken on? Currently I setup an image using the following commands: e.g. view matrix camera 0.98237,-0.066404,-0.17474,86.421,0.014131,-0.90572,0.42363,190.37,-0.1864,-0.41863,-0.88882,-48.082 clip near -10 far 10 position /R:LIG zoom pixel 0.0348 I then save it using: e.g. save 'dir_path/image.png' width 2000 height 2000 supersample 10 transparentBackground False I often will come back to the same cxc script and want to re-render with e.g. a modified pdb file but still want to get exactly the same view. I can then substitute this picture into a figure I've created in e.g. Inkscape without having to resize the image. However I've noticed that often the new image will not have the same zoom (so the model will be bigger and smaller within the total FOV) which means I have to then manually resize it to match what I already have. I've also noticed that if I render on e.g. my laptop rather than my desktop monitors this effects both the zoom as previously mentioned but also the final resolution of the image as this seems tied to the screen resolution. Is there a way to make it so the image will always look the same regardless of hardware etc.? KR, Sam Samuel Haysom Senior Scientist • Protein Sciences Nxera Pharma UK Limited +44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Nxera Pharma UK Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

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ChimeraX adjacent question about AF2 vs AF3
by David S. Fay 09 Jun '25

09 Jun '25

Greetings, I am curious if others have found AlphaFold3 to be slightly worse or less consistent at predicting protein-protein interactions than AlphaFold2. From the AF3 paper it appeared that they were roughly equivalent, with AF3 perhaps having a slight edge. Certainly when it comes to speed and the handling of large proteins, AF3 is far superior. But over time I’ve found a number of cases where AF2 did a better job based on experimentally supported evidence from our lab. Admittedly, this observation is entirely anecdotal and likely prone to bias. And I get that AF2 may predict some interactions better than AF3 and vice versa. But it’s still makes me wonder and I was curious if others had noticed this pattern or had thoughts on the matter. Thanks in advance. David

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copy from Chimera
by Sherwood Casjens 06 Jun '25

06 Jun '25

Sirs: I recently got a new MacBook Pro computer that is running system Sequoia 15.4.1. We loaded ChimeraX version 1.8 (2024-06-10). It seems to work OK except there is no “copy” command in the edit menu and command-C does not copy sequence in the sequence window of Chimera. Any idea what my problem is? Sherwood Casjens Univeristy of Utah

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Q-Score not shown in output file
by Thu Nguyen 05 Jun '25

05 Jun '25

Hi, I am trying to calculate the Q-score of this density map and structure pair using the Q-Score plugin <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxqscore> in ChimeraX and save the score to the output file. I loaded the 2 files to ChimeraX and used this command "qscore #2 toVolume #1 useGui false pointsPerShell 8 shellRadiusStep 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false outputFile /Desktop/q_score.txt" However, the output file is empty and I got the error message in ChimeraX. When I removed the outputFile option, it worked as normal and gave me the average score of .32. Do you know why it happened like this and what I should do to fix it? Thank you very much. Best regards, Thu

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Select all truncated amino acids in model (though ISOLDE?)
by Vorländer,Matthias Kopano 05 Jun '25

05 Jun '25

Hi everyone, Is it possible to create a selector or python script to identify/match all truncated amino acids in a model? If not possible directly in ChimeraX, could ISOLDE offer a solution through matching to residue template “TRUNC_CB”? Thanks in advance, Matthias

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Using measure area command
by jillian.baker＠som.umaryland.edu 04 Jun '25

04 Jun '25

Dear ChimeraX community, I am trying to use the 'measure area' command to measure the area using three atoms (essentially trying to calculate the area of a triangle). I have come up with the script of "measure area #2/b:44@o,97@ca,57@hz3" with 2 being model ID, b being the chain, and then the numbers being residues and the atoms are followed by the "@" symbol. I don't quite get an error here, but I get back "No surfaces specified." I can't seem to figure out away to specify a surface or use a different command to calculate the between these three points. Any help with this would be greatly appreciated. Thanks, Jill

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Align molecule to axes
by Alexander Lee 03 Jun '25

03 Jun '25

Dear ChimeraX community, I have an optimized benzene ring that's floating in space. Is there a way to align that ring to one of the axes' planes so that 2 of the 3 cartesian coordinates read 0,0? Ex: C1 0.00 0.00 z1 C2 0.00 0.00 z2 C3 0.00 0.00 z3 etc Regards, Alex

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Shading from N-terminus to C-terminus?
by Nick Matzke 02 Jun '25

02 Jun '25

Dear ChimeraX list, Thanks so much for this amazing software! I have a kind of obscure question for which I could not find an answer on Google. I've got the FliPQR-FlhB structure, from here: https://www.rcsb.org/structure/6S3L This has 5 copies FliP 1 copy FliR 4 copies FliQ 1 copy FlhB I opened it and am using ribbon view. I've colored the chains by protein type with these commands: color /a,b,c,d,e purple color /f red color /g,h,i,j green color /k yellow Now, I'd like to have each chain shaded from N-terminus to C-terminus, e.g. dark red to light red, or something like that. (I see the rainbow option, but this creates a very complex view if all 11 chains are each an roygbiv rainbow.) Almost as good, is there a way to easily label the N-terminus and C-terminus of each chain? Any suggestions! Thanks so much, Cheers, Nick

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ChimeraX support: Alphafold contacts
by Anthony Newcombe 02 Jun '25

02 Jun '25

Hello I have a commercial license of ChimeraX, I have a question you may be able to help with I have used Structure prediction > Alphafold to predict structures and interactions between 2 proteins and this returned the best_model.pdb But I would like to identify contacts within 8 angstroms, as shown in the Youtube video: https://www.youtube.com/watch?v=TMcjEecFHaI&list=WL&index=26'm typing the command: alphafold contacts /A to /B distance 8 But receive the error: 'Structure best_model.pdb #1 does not have PAE data opened' Do I need to open something? If you can help that would be much appreciated Many thanks Tony Anthony Newcombe PhD Applied Biopharm Consulting Ltd Cork, Ireland http://www.appliedbiopharm.com<http://www.appliedbiopharm.com/> IE: +353 (0)87 3634486 [cid:image001.png@01DBD2E1.AD97E890] Applied Biopharm Consulting Limited is a company located in the Republic of Ireland Reg. No: 747251, VAT No: IE4188817RH. Registered office: Brook Lodge, Lisnacunna, Ballinascarthy, Clonakilty, Cork, Ireland P85 C832. This message is confidential and intended solely for the recipient(s). If you are not the intended recipient, any use, disclosure, copying or distribution of this message or its attachments is strictly prohibited. Please notify the sender immediately by replying to this email and delete the message, its attachments and any copies.

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Comparing Maps
by Abhilash Padavannil 02 Jun '25

02 Jun '25

Hello, I have five different cryoEM maps coming from similar samples. The maps are at different resolutions. I want to compare the density at the region of interest across these maps. How do I normalize the maps say to the first map to make accurate analysis. I know I could scale them using vop scale, but I am wondering which of the parameters I should use. Thanks in advance for your suggestions. Abhilash.

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How to create singlke protein from assembly of 5 individual chains
by Jacek Jagodzinski 29 May '25

29 May '25

Hi, I am medicinal chemist. I used ChimeraX to model missing parts/loops of the protein for which I had cryo-EM structure. It is transmembrane protein consisting of 5 individual chains. I managed to reconstruct missing parts using as a template known sequences of publicly available X-ray structures of proteins and known sequences. I have now a nice assembly of five individual “repaired” proteins perfectly aligned with parts of my cryo-EM structure. However the PDB file of those FIVE individual proteins is not recognized as ONE protein with five separate chains by my other programs. I suppose there is a way to get the result I need, but I cannot find the solution by myself. Can you help? Jacek Jagodzinski, PhD

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Use minimization in chimerax using command line
by TUSHAR GUPTA 29 May '25

29 May '25

Good morning I would like to appreciate your work and efforts in developing and maintaining ChimeraX, it has always been so useful tool in my research. I was initially using Chimera that had excellent feature of using amber force field for energy minimization of structure and making movie using topology and coordinate file. I am working on inducing mutation in nucleic acid and protein structures. I wish to incorporate the minimization step in my research using Chimerax. I will be highly grateful if you could guide me how can I use minimization steps in Chimerax using command line codes. Thank you Tushar Gupta PhD biotechnology Bennett University Greater Noida India "He that can have patience can have what he will." - Benjamin Franklin _____________________________________________ Vineet Jain (Chancellor) Inspiration

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Issue in using vop maximum to make composite map
by Dr. Heng Zhou 29 May '25

29 May '25

Dear ChimeraX developers, I have an issue when using vop maximum command to combine two local maps. Map A and Map B have an overlapping area with each other. The hinge point of structural flexibility is at the center of the overlapping area. Therefore, the left part of Map A and the right part of Map B have a better local density quality, which I want to keep in the composite map. But vop maximum did it on the opposite, resulting in a worse local resolution at the edges of the overlapping area (e.g., Region 1 and 2). Technically, this is not an issue of vop maximium itself. In Region 1, Map A has a better local density quality, while Map B has higher values in some voxels. So the composite map has more voxels derived from Map B in Region 1. Vice versa for Region 2. The only solution in my mind is to split both Map A and B at the hinge point, then do vop maximum for only the left part of Map A and the right part of Map B. But this is time-consuming since I have many local maps to combine. I wonder if you have a better solution? I would appreciate it if you could give advices. Thanks! Best regards, Heng Heng Zhou, PhD | Postdoctoral research fellow Stefan Raunser lab | Structural Biochemistry Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11, 44227 Dortmund, Germany Phone: +49 231-133-2326

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Disulfide bridges
by Pascal Rochaix 28 May '25

28 May '25

Hello, I am a long time user of PyMOL and I am testing ChimeraX for the first time. Is there a simple command to show the disulfide bridges ? It is easy in PyMOL but I don't find it in ChimeraX... Thanks in advance, Pascal Rochaix Protein Scientist www.metafora-biosystems.com<http://www.metafora-biosystems.com> [Logo mail]Pépinière Paris Biotech Santé 29 rue du Faubourg Saint Jacques | 75014 Paris | France

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Working with c-beta truncated models in ISOLDE
by Vorländer,Matthias Kopano 28 May '25

28 May '25

Hi everyone, Is there a way to work with c-beta truncated models in ISOLDE? For truncated residues, Isolde brings up the unparameterized residues dialog, and matches as a possible template the ligand “TRUNC_CB”, which seems reasonable. Since the model also contains complete sidechains, I would not want to rebuild all residues to template, and doing it residue-by-residue is impractical, too. Can the “rebuild to template for all residues of this name” be limited to a selection? Thanks a lot, Matthias

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swapna command extremely slow for large structures
by Vorländer,Matthias Kopano 27 May '25

27 May '25

Dear ChimeraX team, I have noticed that on some structure I am working with, the swapna command is extremely slow, making it almost unusable for structure manipulation. For a single nucleotide substitution, ChimeraX froze for >5 minutes before finishing the operation (that particular structure had ~300 000 atoms). When I however first delete all proteins from the structure, the operation is very fast. What is the rate limiting step in the swapna command? Does it invoke renumbering of all atoms in the PDB file? Without having quantified it, I experienced similar behavior for the build replace command. Would be fantastic if there would be a way to speed this up to increase its usability! Many thanks in advance, Matthias

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Taking control of the string displayed in a pbond associated tooltip
by svle＠tiscali.it 27 May '25

27 May '25

Hi, I have specified some pseudobonds using pbond. It is possible to add a string, conveying other related informations , to that displayed in the tooltip when hovering the mouse on the pseudobond? Also, it is possible to take the complete control of what is displayed in the tooltip? Thanks. Saverio

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How do I get Modeller structure if there was a connection timeout error on ChimeraX?
by Andy Liwang 23 May '25

23 May '25

Dear ChimeraX, I used “Model Loops” on a large protein and even though ChimeraX indicated “Modeller Webservice: 1 of 1 models generated”, it also gave the following error message: modeller refine<help:user/commands/modeller.html#refine> 1:1:all-missing 1/A:1:all-missing numModels 1 fast false adjacentFlexible 1 protocol standard Webservices job id: RO5U9U0YU7YY6TM5 2025-05-23 15:51:56,220 WARNING Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<urllib3.connection.HTTPConnection object at 0x32f0aa350>, 'Connection to webservices.rbvi.ucsf.edu timed out. (connect timeout=None)')': /cxservices/api/v1/chimerax/jobs/RO5U9U0YU7YY6TM5/files Am I able to retrieve the model from webservices.rbvi.ucsf.edu<http://webservices.rbvi.ucsf.edu/>? Sincerely yours, Andy LiWang Professor of Chemistry & Biochemistry University of California Merced, CA 95343

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Problem using pbond
by svle＠tiscali.it 23 May '25

23 May '25

Hi, I would like to use pbond with a pair of atoms. For one of these it is available the model number , the chain ID and the atom serial number. How it is possible to give the atom specification ,having the previous three information, for using it in pbond? Thanks. Saverio

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remotecontrol observations and suggestions
by Roden Deng Luo 23 May '25

23 May '25

Hi, This is to share my observations and practices mainly with people using `remotecontrol xmlrpc`, likely developers. `xmlrpc` has a very high overhead, `remotecontrol rest` with "multipart/form-data" header POST requests should be a better option. First, the REST method can also be used programmatically in scripts or applications fairly easily. I have been sending GET requests using the REST method. Then, I hit "Request-URI Too Long" as I am sending decent sized json data (17KB). Then I tried XML-RPC and realized the frame rate dropped from 58 to 8. The frame rate can be displayed at the status line via `graphics rate true`. Then GPT guided me to try POST with "application/x-www-form-urlencoded" as Content-Type. I got stuck here for a while and found _parse_post <https://github.com/RBVI/ChimeraX/blob/3233aaaf01623ca24bccff7196410401872ce…> returns "fields" in binary and the program could not parse args["command"] <https://github.com/RBVI/ChimeraX/blob/3233aaaf01623ca24bccff7196410401872ce…> as what's inside is b"command". Then I refactored my client to POST with "multipart/form-data" and it worked. More details in my conversations with bots: URL too long: https://chatgpt.com/share/682c856c-174c-8003-bfc9-96fa7e2db0c3 Frame rate cmd: https://chatgpt.com/share/682c8589-2da0-8003-8c14-a59b75927c6b XML-RPC overhead: https://chatgpt.com/share/682c85a7-5f40-8003-8615-095e0a28fccd POST: https://chatgpt.com/share/682c85ca-9938-8003-bb0b-1fb7dd7938ef 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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Commercial vs personal use
by Smith, Timothy 22 May '25

22 May '25

Hello, I previously used ChimeraX for my academic work during my PhD and would like to continue using it for personal use. I do work for a biotech company and while I don't use ChimeraX for work related to my job, I do only have a work issued computer where IT needs to install software. My question is would I still need a commercial license even if I only use it for personal use on my work computer? Thanks, Tim

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1.10 Release Candidates Available Now
by Zach Pearson 21 May '25

21 May '25

Hello ChimeraX users, The first release candidate of ChimeraX 1.10 is available for download today. — Zach

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request help about chimeraX
by Pietro Rizza 21 May '25

21 May '25

hi, thank you for your reply...I hope to explain clearly my problem In attached you will see the file saved with CHIMERA X and I' d like to open my data, in particular SCORE, ENERGY OF POSES in the Biovia Studio DIscover Visualizer....... If you see the second attached.....are reported the several energy of poses (indicated by red arrow) probably I save my data in CHIMERAX IN NOT CORRECT WAY? Why do I not open the energy of poses in Biovia Studio Discover Visualizer? thank you again sincerely Pietro -- ------------------------------------------------------------------------------------------------------------------ Il banner è generato automaticamente dal servizio di posta elettronica dell'Università della Calabria <https://www.unical.it/5x1000>

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Re: request your help about ChimeraX
by Elaine Meng 21 May '25

21 May '25

> On May 21, 2025, at 7:19 AM, Pietro Rizza <pietro.rizza(a)unical.it> wrote: > > Hi Dr Meng > Please you could help me, how do you save the data in CHIMERAX? > How can I save the energy of different poses? > Thanks in advance > Sincerely > Pietro > Hi Pietro, It is better to send questions to the chimerax-users(a)cgl.ucsf.edu address (CC'd here so you don't have to send it again), unless you are including private data. If you send only to me, it may not get answered. I removed your attachment in case it was private, but I see you are using ViewDockX. Of course, the energies and other descriptors of each pose are read from your original input file, so they are already "saved" there, but maybe you are trying to save as a spreadsheet format like CSV? It was not clear from your question. The ViewDockX "Save" button will just save another file that has all of the coordinates as well as the scores (like your original input file). There is no option to save a CSV file from the table, sorry. The only similar possibility is to convert the ViewDockX columns into a model attribute with this recipe <https://rbvi.github.io/chimerax-recipes/vdx_attrs/vdx_attrs.html> ... and then use the "save" command to save an attribute file <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> ... but in my opinion it would be MUCH easier just to process these values from your original input file (the one output by the docking program). You just can't do it with ChimeraX, sorry. Regards, 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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Questions about alphafold interfaces output discrepancies
by Bruno Hay Mele 20 May '25

20 May '25

Hi! I am dabbling with the alphafold interfaces command, and I cannot make sense of the data. In my user case, the table synthesis produced by the command says: Models Confident pairs #Res1 #Res2 4 23 12 12 opening the best model produces these relevant lines in the log 200 atoms, 188 bonds, 24 residues, 1 model selected alphafold contacts last-opened & /A toAtoms last-opened & /B distance 4.0 maxPae 5.0 Found 14 residue or atom pairs within distance 4 with pae <= 5 in the csv, the same model has these relevant columns: distance, max_pae, num_res1, num_res2, num_interface_res1, 4, 5, 246, 246, 20, num_interface_res2, num_interface_res_pairs, num_confident_pairs, 20, 42, 23, interface_res_num1, interface_res_num2 12 values 12 values I am struggling a bit to reconcile all these numbers. The 24 residues selected by chimera after opening are not anywhere else. I suppose these are #Res1 + #Res2 of the synthesis (and interface_res_num1 + interface_res_num2 in the csv)? Both the log synthesis and the csv report 23 as number of confident pairs, but the log message after opening best model says 14 residues (I assume these are those within the distance/pae constraint?) Why Confident pairs is not #Res1 + #Res2? I am also a little bit puzzled by the csv where I read num_interface_res_pairs = 42 and num_interface_res1, num_interface_res2 20 ( I was expecting either 21,21 for num_interface_res or 40 for num_interface_res_pairs. I attach the prediction I was using for diagnosing the problem. cheers, -- Bruno Hay Mele, PhD 2D-20, Biology Dept., University of Naples Federico II https://github.com/bhym/ | +39 081 67 9118

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Smooth MD script vs morph movie
by Alexander Lee 19 May '25

19 May '25

Dear ChimeraX developers, I have been wondering about the pros/cons between the 2 methods to smoothen a trajectory. If I provide a pdb and an nc trajectory file, I can use the smooth_md python script. If the trajectory originally has 100 frames , there will still be 100 frames after using the script. If I exported my trajectory into separate pdb models and morph between each of them, with the default of 50 frames created between each trajectory frame, there will be 5,001 frames after using the command. While importing many pdb's and morphing them takes longer than importing a trajectory and smoothing it, are there any benefits to using either one over the other? I remember seeing some post-production artifacts in smooth_md python script method like the hydrogens of a lysine being in an odd geometry briefly throughout the smoothed trajectory and am unsure if morph command would do the same. Regards, Alex

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Foldseek
by Lynne Howell 15 May '25

15 May '25

Hi Is there an easy way to export the list of similar PDB structures, the % sequence ID, E-value etc that can be found using FOLDSEEK to an excel file. Thanks in advance L __________________________________________________________________________ P. Lynne Howell Canada Research Chair (2006-2020) Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children Professor, Department of Biochemistry, University of Toronto Office and Mailing address: Room 20-9-715 Peter Gilgan Centre for Research and Learning (PGCRL) 686 Bay St. Toronto ON M5G 0A4 Phone: 416-813-5378 (Internal 305378) Web page: https://lab.research.sickkids.ca/howell/ ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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Issues with the 1.9 release on macOS
by Zach Pearson 15 May '25

15 May '25

Hello everyone, I just came across a bug report on our ticket tracker regarding a missing SciPy symbol in the 1.9 release. The basic problem is that scipy has two macOS arm64 wheels up, and one is targeting a higher MACOSX_DEPLOYMENT_TARGET than the other. I think pip ignores this environment variable when selecting packages, so without qualifying that we need the lower deployment target version, pip selects the higher one on our build machines. I fixed this issue a few weeks ago for the 1.10 daily builds, before release candidates went out, so neither of those versions are affected. If you have an ARM Mac and your macOS is less than 14, you should use a daily build or release candidate. You can check your version of macOS by clicking on the Apple logo in the top left, then clicking “About This Mac”. Because we are so close to the 1.10 release, we do not plan to make a 1.9.1 release at this time. Our website will be updated to reflect this information shortly, along with a BlueSky announcement. Thank you, — Zach

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Search in Command History
by Roden Deng Luo 15 May '25

15 May '25

Dear ChimeraX team, Not sure if there is one already, would be great to have a search box in the "Command History" window. 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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Atoms on the other side of the box
by Alexandra Zahradnikova 15 May '25

15 May '25

Dear all, I am trying to minimize the volume of my Gromacs simulation box and therefore in some frames of the trajectory, the atoms appear on the other side of the box. Is there a way to correct this problem in ChimeraX or do I need to resolve it in Gromacs? Best Sasha

2 2

Re: error with trying to open a saved chimera .cxs session
by arangarajan＠initialtx.com 14 May '25

14 May '25

i am trying to open a saved chimerax session saved with version 1.10.dev202504020144 (2025-04-02) using a newly installation of daily build dated 2022-12-30 and i am getting this error : unable to restore session : need to update bundle To restore session: update atomic bundle to ver 1.60.5 or newer ( have 1.43.4) please let me know how to fix this, thanks amith

1 1

Creating a virtual atom n Chimerax
by svle＠tiscali.it 14 May '25

14 May '25

HI, I want to draw a pseudobond between a real atom and the centroid of six carbon atoms. How it is possible define a virtual or pseudo atom with the coordinates of the centroid as one of the ends of the psudobond? Thanks. Saverio

2 2

Re: cif file from pdb-ihm, the integrative structure
by Yaowang Li 13 May '25

13 May '25

Agreed, but has information on proteins and AAs yaowang From: Tom Goddard <goddard(a)sonic.net> Sent: Wednesday, May 14, 2025 9:37 AM To: Yaowang Li <liyaowang2911(a)163.com> Subject: Re: [chimerax-users] cif file from pdb-ihm, the integrative structure Molstar is showing a tube through the beads of the coarse grain model. Tom On May 13, 2025, at 6:28 PM, Yaowang Li <liyaowang2911(a)163.com <mailto:liyaowang2911@163.com> > wrote: Hi Tom The chimerax indeed can open the file, and I succeeded in opening it yesterday, same as you showed. Although the molstar program displays the atomic model, it is hard to analyze. Yaowang <image001.png> From: Tom Goddard < <mailto:goddard@sonic.net> goddard(a)sonic.net> Sent: Wednesday, May 14, 2025 9:17 AM To: Yaowang Li < <mailto:liyaowang2911@163.com> liyaowang2911(a)163.com> Cc: Ben Webb < <mailto:ben@salilab.org> ben(a)salilab.org>; ChimeraX Users Help < <mailto:chimerax-users@cgl.ucsf.edu> chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] cif file from pdb-ihm, the integrative structure Hi Yaowang, You can open the 8zza IHM model in ChimeraX using open 8zza from pdbdev If you get tomorrow's ChimeraX 1.10 release candidate or daily build you could also use open 8zza from pdbihm I just added the database name "pdbihm" because pdbdev was the development name of the IHM repository and is being phased out. As Ben said 8zza is a coarse grain model. Although you will see spheres in the model they do not represent individual atoms. The may represent whole residues or large subunits. Tom IHM 8zza shown in ChimeraX: <image003.jpg> On May 13, 2025, at 6:08 PM, Yaowang Li < <mailto:liyaowang2911@163.com> liyaowang2911(a)163.com> wrote: Hi, Ben and Tom Thank you for your help. “Real structural model” is not the right expression; I mean an atomic model. There should be an atomic model that was generated from the coarse-grained model, and the molstar program on the IHM website can display its atomic model. So it will be perfect that I can open it in Chimerax for viewing this complex structure. In short, I just want to get the atomic model, not the coarse-grained model. Best wishes, Yaowang From: <mailto:chimerax-users-bounces+liyaowang2911=163.com@cgl.ucsf.edu> chimerax-users-bounces+liyaowang2911=163.com(a)cgl.ucsf.edu < <mailto:chimerax-users-bounces+liyaowang2911=163.com@cgl.ucsf.edu> chimerax-users-bounces+liyaowang2911=163.com(a)cgl.ucsf.edu> On Behalf Of Tom Goddard via ChimeraX-users Sent: Wednesday, May 14, 2025 2:01 AM To: <mailto:liyaowang2911@163.com> liyaowang2911(a)163.com Cc: <mailto:chimerax-users@cgl.ucsf.edu> chimerax-users(a)cgl.ucsf.edu Subject: [chimerax-users] Re: cif file from pdb-ihm, the integrative structure Hi Yaowang, As Ben points out 8zza is an integrative hybrid model (IHM). Unfortunately the PDB gives ChimeraX a file with suffix ".cif" for 8zza that does not use the atomic model mmcif dictionary. ChimeraX would need to look at the contents of the file to decide that it is using the IHM dictionary. Currently ChimeraX identifies file types using the file suffix ".cif". That is why it says "No mmCIF models found" when you open this file. I've made a ChimeraX bug report to see if we can improve this <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17661> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17661 ChimeraX is able to read the IHM files. So if you download the 8zza.cif file and open it in ChimeraX with "open ~/Downloads/8zza.cif format ihm" it will show you the coarse grain model. Tom On May 13, 2025, at 8:58 AM, Ben Webb via ChimeraX-users < <mailto:chimerax-users@cgl.ucsf.edu> chimerax-users(a)cgl.ucsf.edu> wrote: On 5/13/25 7:33 AM, Yaowang Li via ChimeraX-users wrote: I am trying to analyze the structures that were deposited in the <https://pdb-ihm.org/> https://pdb-ihm.org< <https://pdb-ihm.org/> https://pdb-ihm.org> Such as the entry: 8zza [...] which is a coarse-grained model, instead of a real structural model consisting of atom coordinates. Could anyone help me figure it out? 8zza is a model of the yeast nuclear pore complex. As you have observed, it is a coarse-grained model, not atomic. I'm not sure what you mean by "real structural model" but the resolution of the data in 2018 was such that only a coarse-grained structure was possible. That's what was deposited and that's what ChimeraX will show you. What are you trying to do? Ben -- <mailto:ben@salilab.org> ben(a)salilab.org <https://salilab.org/~ben/> https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle _______________________________________________ ChimeraX-users mailing list -- <mailto:chimerax-users@cgl.ucsf.edu> chimerax-users(a)cgl.ucsf.edu To unsubscribe send an email to <mailto:chimerax-users-leave@cgl.ucsf.edu> chimerax-users-leave(a)cgl.ucsf.edu Archives: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

2 1

Re: cif file from pdb-ihm, the integrative structure
by Tom Goddard 13 May '25

13 May '25

Hi Yaowang, You can open the 8zza IHM model in ChimeraX using open 8zza from pdbdev If you get tomorrow's ChimeraX 1.10 release candidate or daily build you could also use open 8zza from pdbihm I just added the database name "pdbihm" because pdbdev was the development name of the IHM repository and is being phased out. As Ben said 8zza is a coarse grain model. Although you will see spheres in the model they do not represent individual atoms. The may represent whole residues or large subunits. Tom IHM 8zza shown in ChimeraX: > On May 13, 2025, at 6:08 PM, Yaowang Li <liyaowang2911(a)163.com> wrote: > > Hi, Ben and Tom > > Thank you for your help. > > “Real structural model” is not the right expression; I mean an atomic model. There should be an atomic model that was generated from the coarse-grained model, and the molstar program on the IHM website can display its atomic model. So it will be perfect that I can open it in Chimerax for viewing this complex structure. > In short, I just want to get the atomic model, not the coarse-grained model. > > > Best wishes, > > Yaowang > > > > > From: chimerax-users-bounces+liyaowang2911=163.com(a)cgl.ucsf.edu <chimerax-users-bounces+liyaowang2911=163.com(a)cgl.ucsf.edu> On Behalf Of Tom Goddard via ChimeraX-users > Sent: Wednesday, May 14, 2025 2:01 AM > To: liyaowang2911(a)163.com > Cc: chimerax-users(a)cgl.ucsf.edu > Subject: [chimerax-users] Re: cif file from pdb-ihm, the integrative structure > > Hi Yaowang, > > As Ben points out 8zza is an integrative hybrid model (IHM). Unfortunately the PDB gives ChimeraX a file with suffix ".cif" for 8zza that does not use the atomic model mmcif dictionary. ChimeraX would need to look at the contents of the file to decide that it is using the IHM dictionary. Currently ChimeraX identifies file types using the file suffix ".cif". That is why it says "No mmCIF models found" when you open this file. I've made a ChimeraX bug report to see if we can improve this > > https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17661 > > ChimeraX is able to read the IHM files. So if you download the 8zza.cif file and open it in ChimeraX with "open ~/Downloads/8zza.cif format ihm" it will show you the coarse grain model. > > Tom > > > > >> On May 13, 2025, at 8:58 AM, Ben Webb via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> On 5/13/25 7:33 AM, Yaowang Li via ChimeraX-users wrote: >> >>> I am trying to analyze the structures that were deposited in the https://pdb-ihm.org <https://pdb-ihm.org/><https://pdb-ihm.org <https://pdb-ihm.org/>> >>> Such as the entry: 8zza [...] which is a coarse-grained model, >>> instead of a real structural model consisting of atom coordinates. >>> Could anyone help me figure it out? >> >> 8zza is a model of the yeast nuclear pore complex. As you have observed, >> it is a coarse-grained model, not atomic. I'm not sure what you mean by >> "real structural model" but the resolution of the data in 2018 was such >> that only a coarse-grained structure was possible. That's what was >> deposited and that's what ChimeraX will show you. What are you trying to do? >> >> Ben >> -- >> ben(a)salilab.org <mailto:ben@salilab.org> https://salilab.org/~ben/ >> "It is a capital mistake to theorize before one has data." >> - Sir Arthur Conan Doyle >> >> _______________________________________________ >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>

1 0

cif file from pdb-ihm, the integrative structure
by Yaowang Li 13 May '25

13 May '25

Dear all, I am trying to analyze the structures that were deposited in the https://pdb-ihm.org Such as the entry: 8zza The chimeraX (version 1.7 to 1.10) cannot read the CIF file with warning information warning No mmCIF models found. While it succeeded in opening it after adding the option format ihm. But they are the start model, restraints, and results, which is a coarse-grained model, instead of a real structural model consisting of atom coordinates. Could anyone help me figure it out? Best wishes

3 2

Re: Samsung 27" Odyssey 3D G90XF 4K 165Hz Monitor
by Tom Goddard 12 May '25

12 May '25

Hi Gökhan, The Samsung web page you referenced says the monitor is $3000, the same price as the Acer 27", and the Samsung also uses eye-tracking so it will probably only work for one person. The Sony and Acer displays both use OpenXR and eye tracking. This is good and bad. The good part is as you move your head to the side you see the side of the rendered objects. The bad is that most 3D applications do not support OpenXR unless they are VR applications. In contrast the Samsung uses side-by-side video input. That allows it to work with any 3D application that supports that common 3D format. Here's a description on Reddit talking about side-by-side input with the Samsung. (Unfortunately the Samsung manual does not say much.) https://www.reddit.com/r/Monitors/comments/1k8wnqa/samsung_odyssey_3d_g90xf… The drawback of the Samsung approach is that the monitor has no way to tell the application (e.g. ChimeraX) that your head has moved to the side (that is what OpenXR does). So when you move your head to the side you just see the same view direction of the 3D object only skewed. It's not a disaster, you can rotate the molecule if you want to see it from the side. The Samsung manual says only Windows is supported since they include some crappy software that runs on your Windows machine. I'm not sure if it is needed to handle side-by-side input. I'd love to see the Samsung display. It uses a 4K panel like the Sony and Acer. Like those displays it must be using a lenticular grating to send some pixels to your left eye and some to your right eye so the actual resolution in 3D is more like HD (2K). Still that is pretty good. (With old technology LCD shutter glasses you would get full 4K resolution since the two eye images use all screen pixels and just alternate in time.) If I had one of these displays I think I could make ChimeraX render full-screen side-by-side. Since you can't drag the ChimeraX graphics into a separate window I would try to add code to create a separate window and render to it as an option. My lab does not have money to spare to buy such a display (NIH funding problems), so don't expect to work on this. Tom > On May 7, 2025, at 11:19 PM, <tolung.bio(a)gmail.com> <tolung.bio(a)gmail.com> wrote: > > Hi Tom, > > This Samsung is less than half the price (27” for 2K USD) compared to the SONY in the review. > > Let me know if you can score one of these to test/develop for :) > > Cheers, > > Gökhan > > > From: Tom Goddard <goddard(a)sonic.net> > Sent: Thursday, 8 May 2025 8:45 AM > To: tolung.bio(a)gmail.com > Cc: chimerax-users(a)cgl.ucsf.edu > Subject: Re: [chimerax-users] Samsung 27" Odyssey 3D G90XF 4K 165Hz Monitor > > Hi Gökhan, > > There is no ChimeraX capability to make the graphics pane full screen, so it will not work with a 3D display that wants full-screen side-by-side stereo format. The graphics pane is not a docked panel like the other ChimeraX tools. The ChimeraX main window is a Qt QMainWindow which treats that center area specially and it cannot be detached into a floating window. I'm not sure how hard it would be to allow that. > > We are also working on glasses-free eye-tracked 3D displays such as the Sony Spatial Reality and Acer SpatialLabs displays. They use OpenXR and only work on Windows and only with 1 person viewing, and costly $3000-5000, so they have some limitations. Here's a description of trying the Sony 3D display with ChimeraX > > https://www.rbvi.ucsf.edu/chimerax/data/sony3d-mar2025/sony3d.html > > Tom > > > >> On May 7, 2025, at 12:24 AM, Gokhan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Hello ChimeraX team and users, >> >> Does ChimeraX support this monitor? >> >> https://www.samsung.com/au/monitors/gaming/odyssey-3d-g90xf-27-inch-165hz-u… >> >> I read a very positive review about this monitor and may consider buying one if it works with ChimeraX. >> >> The review says that this monitor needs a full-screen side-by-side output. Just as many of the sub-windows of ChimeraX can be docked and undocked (e.g., log, Models, etc.), is there way to ‘undock’ the main graphics window to make it full screen? Or, is there a way to display the graphics window on a secondary monitor as a full-screen output? >> >> Thanks, >> >> Gökhan >> >> _______________________________________________ >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

3 10

Samsung 27" Odyssey 3D G90XF 4K 165Hz Monitor
by tolung.bio＠gmail.com 07 May '25

07 May '25

Hello ChimeraX team and users, Does ChimeraX support this monitor? https://www.samsung.com/au/monitors/gaming/odyssey-3d-g90xf-27-inch-165hz-uh d-ls27fg900xexxy/?srsltid=AfmBOopLIkVAywsvNylPGVRL3wUoUJuBvUOPOz0metBjwLM2Nn xgmQVf I read a very positive review about this monitor and may consider buying one if it works with ChimeraX. The review says that this monitor needs a full-screen side-by-side output. Just as many of the sub-windows of ChimeraX can be docked and undocked (e.g., log, Models, etc.), is there way to undock the main graphics window to make it full screen? Or, is there a way to display the graphics window on a secondary monitor as a full-screen output? Thanks, Gökhan

2 1

including HET atoms in kvfinder calculations from ChimeraX
by Elaine Meng 07 May '25

07 May '25

> On May 7, 2025, at 2:01 AM, Mühleip, Alexander <alexander.muhleip(a)helsinki.fi> wrote: > > Hi Elaine, > > I am checking out the new kvfinder tool in ChimeraX. I was wondering if there is some way to prevent it from disregarding heteroatoms in the cavity search (in my eyes, e.g. excluding hemes is not helpful). I tried changing the selection syntax, but I think the pruning is taking place internally in kvfinder. > > Is there some way to interfere with it or make an ignore option (like the isolde implementation in chimerax has)? > > Best wishes, > Alex > > Alexander Mühleip > group leader > HiLIFE-Institute of Biotechnology > University of Helsinki > Finland > +358503282167 Hi Alex, Generally it's better to ask on the chimerax-users list, since as the resident non-programmer I often don't know implementation details. I CC'd the list in case others may also be interested in this topic. After consultation with the programmer who implemented this tool, we could not think of any current workaround. It uses the "main" category of atoms (definition in link below) which is automatically assigned cannot be manually overwritten. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#surfcats> However, we can consider this a request for enhancement that might be added in the future. Best wishes, 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

Options to align two models and calculate per-residue RMSD
by christian.steinmetzger＠imbim.uu.se 07 May '25

07 May '25

Dear ChimeraX users, I'm working with some different ribosome structures which I first want to align to a reference structure (as rigid bodies) and then calculate RMSD values with respect to the reference. The number of chains are the same between my structures and the reference, and the chain names + residue numbers are congruent as well. However, some of my chains have residues missing or added at the ends, have a small number of insertions (using insertion codes in the pdb file) or point mutations. What I have tried so far is: "matchmaker #2 to #1 pairing ss show true" "save file.defattr #2 attrName r:seq_rmsd modelIds false" (to store the resulting RMSD values for later use) which aligns based on CA for protein chains and C4' for RNA. I haven't given any explicit chain specification (each model has 56 chains). Am I correct to think that the RMSD values I get are based on a whole-structure rigid-body alignment that takes all chains into account simultaneously? Or does it align each chain in #2 to its matching chain in #1 individually? For the proteins I think per-residue CA-RMSD values are suitable for what I need, but for the RNA chains I would like to get per-residue all-atom RMSDs, not just C4'. Can this be achieved with matchmaker? I have also tried to use the align command like this: "align #2 toAtoms #1 each structure matchChainIds true matchNumbering true" which, to my understanding, would do the alignment not just based on CA/C4', but for all atoms. Is that correct? With this, what would be the best way to extract per-residue RMSD values? The "rmsd" command rightfully complains about unequal numbers of atoms between #1 and #2. Is there a way to implicitly select only the atoms that are congruent between #1 and #2? Kind regards, Christian

2 2

RMSD for all frames in a trajectory
by Alexandra Zahradnikova 07 May '25

07 May '25

Dear All, I am working with a trajectory of a tetramer. I would like to align the A chains in all frame of the trajectory and then calculate the rmsd of all chains in all frames relative to the respective chain of the first frame (i.e., align only chains A but calculate for all chains), and write the results to a text file. Is that possible? I can do a similar calculation with a script in old Chimera but don’t know how to do it in ChimeraX. I attach the zipped script for old Chimera. Best regards Sasha

2 6

Re: [Chimera-users] Add sequence logo to view
by Elaine Meng 05 May '25

05 May '25

Hi Alex, Sorry no we do not have a feature like that currently. (P.S. It may be better to use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address CC'd here for ChimeraX questions.) In ChimeraX: The most similar thing I can thihk of is that for deep mutational scanning results it is possible to show labels with the scores of each residue type shown in a color-coded grid, but the "rub" is that you would have to open the data from a specific format we are using for these kinds of results: mutation scores format: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/mutationcsv.html> I could imagine that instead the sequence alignment profile at each position could be shown as a similar label. ChimeraX has a new profile-grid viewer for sequence alignments as an optional alternative to the standard viewer, <https://rbvi.ucsf.edu/chimerax/docs/user/tools/profilegrid.html> .... so such a label could essentially be the profile column rearranged into a squarish grid, as in the mutational scanning labels image above. However, that has not yet been discussed (nor implemented, of course). We do not have any sequence logo type of display. Regards, 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 May 5, 2025, at 7:35 AM, Alexander Lee via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear ChimeraX community, > > I have a consensus sequence + logo done in an outside program. Is there a way to superimpose this onto a crystal structure? When hovering my mouse over a residue in the structure viewer (or sequence viewer), I would like the logo to come up. Is there a similar feature available? > > Regards, > Alex > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

1 0

How can I overlay the 2Fo-Fc density map onto the amino acid residues I specified?
by 1025049892＠qq.com 04 May '25

04 May '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.

4 5

Morphing of structures with different chain numbers
by Enrico Martinez 01 May '25

01 May '25

Dear ChimeraX Users, I am trying to perform a morphing between two cryo-EM structures of the same complex, where one structure has twice the number of chains as the other (PDBs 3J9K and 8Y6Q). However, the larger structure causes an error during morphing. I have attempted to write a script that aligns the two structures and deletes the unmatched chains from the larger structure. Unfortunately, the script is not working as expected. from chimerax.core.commands import run def delete_unmatched_chains(session): # Get models #1 and #2 m1 = next((m for m in session.models if m.id == (1,)), None) m2 = next((m for m in session.models if m.id == (2,)), None) if m1 is None or m2 is None: session.logger.info("Model #1 or #2 not found.") return chains1 = {chain.chain_id for chain in m1.chains} chains2 = {chain.chain_id for chain in m2.chains} unmatched = chains1 - chains2 if unmatched: chain_ids = ",".join(unmatched) # Deleting unmatched chains run(session, f"delete /{chain_ids}") session.logger.info(f"Deleted chains: {', '.join(unmatched)}") else: session.logger.info("No unmatched chains found.") Could you please help me or alternatively propose another solution? Any suggestions would be greatly appreciated. Thank you in advance ! Enrico

3 6

Saving Images with Specific Dimensions and DPI in ChimeraX
by svle＠tiscali.it 30 Apr '25

30 Apr '25

Hi, In Chimera, when saving an image, it's possible to specify the output size in centimeters and the resolution in DPI. This feature is very useful for preparing figures for theses and publications. Is it possible to do the same in ChimeraX? I've read the documentation for the save command, but it's not entirely clear to me how to achieve this. Do you have any suggestions? Best regards, Saverio

2 3

Reproducing the Chimera Preset Publication 5 ( flat ribbon ) in ChimeraX
by svle＠tiscali.it 29 Apr '25

29 Apr '25

Hi, it is possible to reproduce the Chimera Preset Publication 5 ( flat ribbon ) in ChimeraX? What are the commands to use in order to have this type of preset in ChimeraX? This is a very nice preset. Thanks. Saverio

2 2

How to apply symmetry I to generate an icosahedron model
by 唐延婷 29 Apr '25

29 Apr '25

Hi doctor, when I open a map (ID 1) and a model (ID 2), the map is the whole icosahedron while the model is the protomer of the icosahedron. I want to apply symmetry I to generate an icosahedron model. I have rotated and translated the model into a reasonable position inside the map and then done a “fit in map” to get the initial placement for sym. Then I enter a command ''measure center #1''，center of mass xyz coordinates for map_sharp.mrc = (238.08, 238.08, 238.08)，enter another command ''sym #2 I,222 center 238.08, 238.08, 238.08'' I can see an icosahedron model fit in map. But when I save the icosahedron model.pdb, I found the icosahedron model actually is the model of the protomer. How can I apply symmetry I to generate a true icosahedron model, used for subsequent model refine in coot and real_space_refine in Phenix. Thank you very much. Best wishes! yanting 延婷 yanting.tang(a)mail.nankai.edu.cn

2 2

Issues with find cavities tool
by Marino, Claudia 28 Apr '25

28 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 11

reduce gridpoints on the cryoEM map (640 x 640 x 640 ) to ( 320 x 320 x 320)
by arangarajan＠initialtx.com 28 Apr '25

28 Apr '25

hi, i need to reduce the grid points to make the map work with MOE. I am not sure if this is possible in chimerax and i would appreciate some suggestions for creating a mrc file with reduced grid points. please let me know your thoughts. best amith

2 2

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

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

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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

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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.

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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

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!

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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 __________________________________

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

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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

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

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

Re: ChimeraX-users Digest, Vol 99, Issue 28
by Boaz Shaanan 16 Mar '25

16 Mar '25

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: 1. Omit the cofactor from the pdb2pqr and APBS. 2. Read into chimerax the complete pdb (i.e. including the cofactor). 3. Generate the surfaces (protein and cofactor). 4. Render the electrostatic potential on both surfaces (i.e. Cofactor and protein surrounding it) and probe the potential on the cofactor. 5. 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 Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il ________________________________ From: chimerax-users-request(a)cgl.ucsf.edu <chimerax-users-request(a)cgl.ucsf.edu> Sent: Friday, 14 March 2025 21:00 To: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> Subject: ChimeraX-users Digest, Vol 99, Issue 28 Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..." Today's Topics: 1. sybyl vs amber atom types in ChimeraX (laurene.jacquot) 2. Re: sybyl vs amber atom types in ChimeraX (David A Case) ---------------------------------------------------------------------- Message: 1 Date: Fri, 14 Mar 2025 09:47:39 +0000 From: "laurene.jacquot" <laurene.jacquot(a)etu.chimieparistech.psl.eu> Subject: [chimerax-users] sybyl vs amber atom types in ChimeraX To: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> Message-ID: <MR1P264MB2612AFE1D7D6BEF80D0B069A92D22(a)MR1P264MB2612.FRA P264.PROD.OUTLOOK.COM> Content-Type: multipart/alternative; boundary="_000_MR1P264MB2612AF E1D7D6BEF80D0B069A92D22MR1P264MB2612FRAP_" 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 -------------- next part -------------- A message part incompatible with plain text digests has been removed ... Name: not available Type: text/html Size: 3823 bytes Desc: not available ------------------------------ Message: 2 Date: Fri, 14 Mar 2025 09:08:36 -0600 From: David A Case <dacase1(a)gmail.com> Subject: [chimerax-users] Re: sybyl vs amber atom types in ChimeraX To: "laurene.jacquot" <laurene.jacquot(a)etu.chimieparistech.psl.eu>, chimerax-users(a)cgl.ucsf.edu Message-ID: <20250314150836.x2iskz4ufcygpsqt(a)pop-os.localdomain> Content-Type: text/plain; charset=us-ascii; format=flowed On Fri, Mar 14, 2025, laurene.jacquot via ChimeraX-users wrote: > >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. I don't have a ChimeraX answer here, but rather a question: why do you need a protein mol2 file with Amber atom types? Amber workflows would not create a mol2 file for an entire protein; but of course, you may need such a file for some other purpose. If so, we may be able to find some Amber tools that does this (or avoids needing it), if the ChimeraX folks themselves don't have a solution. ....dave case ------------------------------ Subject: Digest Footer _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu Archives: https://protect.checkpoint.com/v2/r02/___https://mail.cgl.ucsf.edu/mailman/… ------------------------------ End of ChimeraX-users Digest, Vol 99, Issue 28 **********************************************

2 1

Ubuntu 24 ARM Daily Builds
by Zach Pearson 15 Mar '25

15 Mar '25

ARM daily builds for Ubuntu 24.04 are now available. — Zach

1 0

Feature suggestion: cubic interpolation for image display
by Ricardo Righetto 14 Mar '25

14 Mar '25

Dear ChimeraX team, (I have a vague memory of discussing this before, apologies if duplicate!) When displaying volumes as images (e.g. cryo-ET volume slices), I see that by default it uses linear interpolation: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#style Would it be possible to offer higher-order interpolation options such as cubic? I love how customizable it is to make figures in ChimeraX, but this is the one feature that we really miss compared e.g. to 3dmod from IMOD. Thank you! -- Ricardo Diogo Righetto

2 7

Dockprep Inquiry
by Emir MALOVIC 13 Mar '25

13 Mar '25

Hello, I am trying to perform some simple docking between a small molecule and a protein. I get the following warning: (UNL) `bash.exe: warning: could not find /tmp, please create!` I was browsing around and noticed I may need to set up ChimeraX Development Environment. Is this true? Thank you, Emir

2 1

ISOLDE refine.eff and phenix.refine
by Shawn Rumrill 13 Mar '25

13 Mar '25

Dear ChimeraX Community, Not strictly ChimeraX related, but probably interesting to some and I've seen some feedback for ISOLDE here... I am using ISOLDE to rebuild a mid-resolution protein/NA model (still adjusting to using ISOLDE, but really powerful tool). I want to refine using phenix.refine, but I am running into a problem with the refine.eff file. The error from the terminal output is below. I've gathered that this is due to a change in parameter terminology from Phenix 1.20 to 1.21. My question is, is there some way to write the refine.eff file with the required information? I would hate to have to manually edit the .eff output file each time I want to run a new refinement in Phenix. Thanks, Shawn Error: Processing files: ------------------------------------------------------------------------------- Found phil, refine.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ refine.eff Unrecognized PHIL parameters: ----------------------------- refinement.input.pdb.file_name (file "refine.eff", line 6) refinement.input.xray_data.file_name (file "refine.eff", line 9) refinement.input.xray_data.labels (file "refine.eff", line 10) refinement.input.xray_data.high_resolution (file "refine.eff", line 11) refinement.input.xray_data.low_resolution (file "refine.eff", line 12) refinement.input.xray_data.r_free_flags.file_name (file "refine.eff", line 14) refinement.input.xray_data.r_free_flags.label (file "refine.eff", line 15) refinement.input.xray_data.r_free_flags.test_flag_value (file "refine.eff", line 16) Sorry: Some PHIL parameters are not recognized by phenix.refine. Please run this program with the --show-defaults option to see what parameters are available. PHIL parameters in files should be fully specified (e.g. "output.overwrite" instead of just "overwrite")

2 1

Re: Inquiry to docking protein onto lipid bilayer
by You, Youngki 12 Mar '25

12 Mar '25

Hello Tommy, You can use this server (PPM in OPM site), https://opm.phar.umich.edu/ppm_server3_cgopm , to determine the orientation and depth of your protein in the membranes. After that, you can use the model from PPM in CHARMM-GUI. Best, Youngki ________________________________PNNL__ Youngki You, PhD Post Doctorate RA, Biochemical Mechanisms Structure, Function & Design Biological Sciences Division Pacific Northwest National Laboratory Tel: +1 (509) 371-6660

1 0

Inquiry to docking protein onto lipid bilayer
by Tommy Tong 12 Mar '25

12 Mar '25

Dear ChimeraX experts, Good afternoon. My name is Tommy from San Diego Biomed. I am a beginner to ChimeraX version 1.9. May I ask if it is possible to use ChimeraX to dock a membrane protein into a lipid bilayer? I obtained Phosphotidylcholine bilayer (POPC) structure from CHARMM-GUI webpage https://charmm-gui.org/?doc=archive&lib=lipid_pure, and was wondering if it is possible to “place” a protein into this POPC structure in ChimeraX. Your help and advice on this is greatly appreciated. Thank you. Sincerely, Tommy

2 1

Obtain individual RMSD values
by javisanchezdelrio＠gmail.com 12 Mar '25

12 Mar '25

Hello, I have an issue when applying matchmaker command in ChimeraX. When I execute the command: matchmaker #1 to #2 showAlignment true I obtain the alignment with the bars in the upper layer showing the individual RMSD of each residue. But the results yields the overall RMSD of the alignment (i.e. RMSD between 108 pruned atoms). Is there any way to obtain those individual RMSDs of the alignment as a file or have them printed in the log for post-processing? Thank you in advance

3 2

Dividing a huge model (& map) into smaller chunks
by Alejandro Buschiazzo 12 Mar '25

12 Mar '25

Dear chimeraX developers/users Using version 1.9, I am trying to divide a very big mmcif model (230K + nonH atoms; >130 chains) and corresponding mrc map, into a number of smaller mmcif files (and corresponding cropped maps, covering just those parts). What I’ve tried so far unsuccessfully: I can create dummy atoms with build start atom, at desired x,y,z points, so that I can then use select zone to select a radius and keep parts near each dummy atom. Yet, that is suboptimal: I would largely prefer to keep (build) boxes, and not spheres, ensuring complete recovery and no blind spots. So that each box slightly overlaps with the neighboring one, and systematically covers the whole original map volume. 1. How can I generate a script that will do this "systematic windowing” screening, making boxes of a defined side-length at each step, and keeping the model within? 2. How should I then crop the original map, so that it covers each box (with a small padding on the borders)? 3. How should I stitch back the models, so that I don’t loose any atomic coordinates information? (of course that stitching will be done after I do some refinement work on each boxed model vs map) So sorry for the many questions! I’ve been trying hard to find this kind of strategy, and just can’t seem to succeed…. Thank you very much in advance Alejandro -- Alejandro Buschiazzo, PhD Associate Professor Laboratory of Molecular & Structural Microbiology Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 ext. 120 Fax: +598 25224185 https://pasteur.uy/en/laboratories/molecular-and-structural-microbiology/

2 4

General ?s - Foldseek (Sequence Plot) and Similar Structures Table
by Emir MALOVIC 11 Mar '25

11 Mar '25

Hello, Quick question: When I load the sequence plot, I receive 2 sequence images separated by a very large black space. When I save the image as a PNG, the black space between the sequence images is retained. Basically, the image is mostly black space. Is there a way to change that or is this a bug? Am I able to somehow copy the Similar Structures table or export it into Excel? A copy/paste function would be ideal and quick. I am using the Chimera 1.10 dev. Please let me know at your earliest convenience! Thank you, Emir

2 3

Suggestion for improvement
by James Raymond 11 Mar '25

11 Mar '25

I love ChimeraX and use it often for my work, e.g. this one <https://www.pnas.org/doi/10.1073/pnas.2421910122>. When using AlphaFold to predict protein structure, the sequence is pasted into the sequence box. It does not allow entering the fasta name ">name" before the sequence.. Allowing a name to be included can avoid much confusion. Presently, the screen shows the output as "best_model" which becomes very confusing when several best models are shown on the screen. James Raymond Univ. Nevada Las Vegas

3 3

What is the .exe file for ChimeraX Toolbox?
by m.i.bashir＠bham.ac.uk 11 Mar '25

11 Mar '25

Hi all, First time posting here. I'm looking to find the name and location of the file/folder that manages the ChimeraX in-app browser. The way I launch the browser is to go to 'tools' in the top bar, then press 'more tools', and then it brings up the ChimeraX Toolshed Where is the .exe file that controls this in app browser? I am attempting to find the .exe file and black list it, so we can use ChimeraX for an exam Thanks,

4 3

SASA in MDS
by Gabriel López Velázquez 10 Mar '25

10 Mar '25

Dear Elaine, I am sorry; I did not state the subject of my previous email. I would ask for help. How can I calculate SASA as a function of time from the MD simulations in Chimerax? What archives need to perform it? Thanks in advance! Gabriel.

2 2

(no subject)
by Gabriel López Velázquez 10 Mar '25

10 Mar '25

Dear Elaine, I would ask for help. How can I calculate SASA as a function of time from the MD simulations in Chimerax? What archives need to perform it? Thanks in advance! Gabriel.

1 0

Inquiry About Favorable Contacts and Display Methods in ChimeraX
by 田畑　健士郎 07 Mar '25

07 Mar '25

Subject: Inquiry About Favorable Contacts and Display Methods in ChimeraX Dear ChimeraX Developers, My name is Kenshiro Tabata. I hope this email finds you well. I am currently using ChimeraX to analyze the effects of point mutations on protein structure, particularly in cases where a larger side chain (e.g., methionine) is replaced by a smaller one (e.g., valine). In such cases, I expect that interactions with the opposing amino acids may be reduced due to the decreased side-chain volume. To investigate this, I would like to ask for your guidance regarding the interpretation and visualization of favorable contacts. ________________________________ 1) Understanding Favorable Contacts I understand that the contacts command identifies all types of interactions, whereas the clashes command detects only unfavorable interactions. Based on this, I interpreted the positive VDW overlap as indicating unfavorable (repulsive) interactions, while an overlap between 0 and -0.4 represents favorable (attractive) interactions. Could you confirm if this understanding is correct? ________________________________ 2) Best Approach for Displaying Only Favorable Contacts To analyze how the mutation affects interactions, I would like to display only favorable contacts. Below is the approach I have considered: Proposed Approach 1. Retrieve all interactions (favorable, neutral, and unfavorable) using the contacts command contacts overlapCutoff -0.4 saveFile all_contacts.txt 2. Retrieve only neutral and unfavorable interactions contacts overlapCutoff 0 saveFile non_favorable_contacts.txt 3. Compute the difference between these two sets using Python, extract only favorable contacts, and format them into a ChimeraX pseudobond file # File paths all_contacts_path = "all_contacts.txt" non_favorable_contacts_path = "non_favorable_contacts.txt" favorable_contacts_path = "favorable_contacts.pb" # Read files with open(all_contacts_path, "r") as f: all_contacts = set(f.readlines()) with open(non_favorable_contacts_path, "r") as f: non_favorable_contacts = set(f.readlines()) # Extract favorable contacts favorable_contacts = all_contacts - non_favorable_contacts # Convert to ChimeraX pseudobond file format with open(favorable_contacts_path, "w") as f: f.write("; Pseudobond file for favorable contacts\n") f.write("; radius = 0.1\n; color = green\n; dashes = 6\n") for line in favorable_contacts: parts = line.strip().split() if len(parts) >= 4: atom1 = f"/{parts[0]}:{parts[1]}@{parts[2]}" atom2 = f"/{parts[3]}:{parts[4]}@{parts[5]}" f.write(f"{atom1} {atom2}\n") 4. Load the extracted favorable contacts into ChimeraX for visualization open favorable_contacts.pb Would this be an appropriate approach? Alternatively, is there a simpler or more precise way to achieve this in ChimeraX? I appreciate your time and assistance, and I look forward to your advice. Best regards, Kenshiro Tabata

2 3

AI in ChimeraX
by Elaine Meng 07 Mar '25

07 Mar '25

On Mar 7, 2025, at 6:01 AM, Veach, Kevin G. <kevin.veach(a)uky.edu> wrote: > > Hi Elaine: > Does Chimera-X use Artificial Intelligence or Large Language Learning Models? > Thank you, > > Kevin > Kevin Veach, Computer Support Specialist II > University of Kentucky, Animal & Food Sciences Dept. Hi Kevin, Please use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address CC'd here for general questions about ChimeraX -- I'm not the top expert on all parts of ChimeraX, so you may get better answers from other developers or our user community. Regarding your question, my understanding is that ChimeraX itself does not use these kinds of calculations, but it has tools that interface to web services or other calculations (run outside of ChimeraX) that do use them. The ones that I can think of are AlphaFold/ColabFold and ESMFold: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html#predict> 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

Creating movie in ChimeraX from YASARA simulation
by ibogdanov 07 Mar '25

07 Mar '25

Hi ! I have the following question - How can I create a movie, when I cannot use the YASARA.sce file from which I converted/extracted xtc.file(the trajectories) when I have all the snapshots(pdb and sim.files) created as separate files during the performed simulation in YASARA...I've uploaded for example the first pdb file of the series and the xtc.file but isn't the saved xtc.file(trajectories) of the whole simulation(for all the structures)? How would you suggest me to solve this problem, if ChimeraX doesn't support sce.files ? Thank you in advance! Kind Regards, Ivan Bogdanov

2 2

Problem installing on OSX
by Thom Hughes 06 Mar '25

06 Mar '25

I apologize for the dumb question, but here it is. I want to install the isolde extension. When I go to more tools, isolde, and click the install button a .whl file downloads correctly. But then nothing happens. I’m running OSX 15.3.1. thanks in advance for any pointers!

2 4

Unable to open the file after downloading ChimeraX
by Guo-Ping Zhou 05 Mar '25

05 Mar '25

Dear Sir/Madam, After downloading ChimeraX, I automatically get the attached .png in the application as a microsoft word file. However, I can't open the Quick Access Toolbar. Could you please tell me how to make it work? Thanks! Guo-Ping Zhou, Rocky Mount Life Sciences Institute, Rocky Mount, NC 27804

2 1

(no subject)
by FRANGIE Christian 05 Mar '25

05 Mar '25

Dear UCSF ChimeraX Support Team, My name is Christian frangieh, I am currently using Chimera X to visualize my AlphaFold simulations, and I want to check when i introduce a mutation and change one residue (amino acid), whether there is a change in the surface accessibility of the residue. Currenlty i am checking this visually by checking whether the residue is exposed to the surface or hidden. Nevertheless, i would like to know how can i do this with a command or by some form of calculation or structural analysis. Can you please help me with this matter? Warm Regards, Christian

2 2

Can not find Structure Minimization in ChimeraX menu
by N.B. Nugroho 04 Mar '25

04 Mar '25

Dear ChimeraX developers I a little bit confuse to find the Structure Minimization menu in ChimeraX. In Chimera 1.16 it located in menu Tools>Structure Editing>Minimize Structure. Could you please guide me for this little problem. Best regards Nuki B Nugroho

2 1

(no subject)
by junjie han 02 Mar '25

02 Mar '25

Hi, I hope you are doing well. May I ask two questions? First one: Why does the connection part between the side chain and backbone, which is circled in a dashed line in ChimeraX, look so abnormal? How can I make it display normally? [cid:437c0c59-2e31-4251-ac9c-eff3f64af0dd] Second one: Is it possible to show the border only for a specific region of protein without hiding other regions? Thanks, Junjie

2 1

define integer attributes for multiple individual pseudobonds
by hannes.ludewig＠googlemail.com 28 Feb '25

28 Feb '25

Dear developers, I am trying to color pseudobonds by an individual (per-bond) attribute value (integer). I seem to be unable to use .pb files to create individual pseudobonds. And when I am using the pbond command several times providing an individual name for each pseudobond thus creating individual models (#1.1, #1.2, etc) I am unable to assign an attribute and color all pseudobonds according to the corresponding attribute value. What I want to create is similar to the alphafold contacts colored by PAE. Only that the values I am providing aren't PAE and I would like to determine the residue pairs that form each pseudobond. I apologize in case I am overlooking something obvious, but your help and/or clarification would be very much appreciated. Thank you. Best wishes, Hannes

3 2

Disulphide bridges in ISOLDE
by Guillaume Gaullier 28 Feb '25

28 Feb '25

Hello ISOLDE users and Tristan, Is there a distance threshold at which ISOLDE won't let me close a disulphide bridge? I am puzzled, because it seems I can close a disulphide between two Cys about 10 residues apart in sequence and quite far from each other in space. In fact much further apart than a bond length, so the resulting bond looks ridiculously stretched. But it is quickly fixed when running a local simulation, even if it needs to pull the backbone out of density to achieve a reasonable S-S bond length. In the same model, I have two other Cys that follow each other in sequence. When loading the AlphaFold prediction, the two S atoms are close enough (for some reason) that ISOLDE offers to make the disulphide, so I say yes. Later on, wanting to test both options to assess which one is best supported by the map, I can break this disulphide, but once I do there is no way to close it again. In this case, the two S atoms settle about 3.4 Å apart when removing the bond, which is longer than an ideal disulphide, but much shorter than the distance over which ISOLDE still allowed me to form a disulphide in the first case. The documentation doesn't say anything about disulphides (or somehow I missed it). In fact, there seems to be no command to operate on disulphides? Using the menu item does not write anything to the Log, so if there is a command I cannot find what it is and what options it might accept. If someone can help with this, I would appreciate it! Thank you, Guillaume --- Guillaume Gaullier, PhD Researcher, Blikstad group Molecular Biomimetics / Microbial Chemistry Department of Chemistry - Ångström Uppsala University Lägerhyddsvägen 1 752 37 Uppsala Sweden 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

3 6

Assistance Required: Extracting List of Interacting Residues within 4 Å in UCSF Chimera
by Rashmi Aggarwal 27 Feb '25

27 Feb '25

Dear UCSF Chimera Support Team, I hope this message finds you well. I am currently working on analyzing interactions between two molecular structures using UCSF Chimera. I have successfully identified residues that are within a 4 Å distance between the two molecules. However, I am encountering difficulties in obtaining a clear, textual list of these interacting residues, as reading them directly from the visual representation is challenging. Could you please provide guidance on the specific commands or procedures within Chimera that would allow me to: 1. *Select residues* in one molecule that are within 4 Å of the other molecule. 2. *Generate and export a list* of these selected residues for further analysis. I have attempted various selection and reporting commands but have not yet achieved the desired outcome. Detailed instructions or references to relevant documentation would be greatly appreciated. Thank you very much for your assistance. Best regards, Rashmi

2 2

Show side chain, main chain, and cartoon at the same time
by Zhang, Miao 27 Feb '25

27 Feb '25

Dear colleagues I am new to ChimeraX. I am trying to figure out how to show side chain, main chain, and cartoon at the same time in a protein structure. Like the one below made in other software. Could you please help? [cid:image001.png@01D9D154.CE3D4440] Best, - - - - - - - - - - - - - - - - - Miao Zhang Ph.D. Associate Professor Chapman University School of Pharmacy 9401 Jeronimo Rd, Suite 297W Irvine, CA 92618 Phone: 714-516-5478 http://www.chapman.edu/our-faculty/miao-zhang

2 24

Cannot click popup windows in ChimeraX WSL installation
by Jobichen 26 Feb '25

26 Feb '25

Hi All,I am unable to click on any popup windows in my chimeraX installation. For eg: colour menu, once popped up, unable to click on any options.Ubuntu 22.04.5 LTS installed under WSL in Dell laptop. ChimeraX ver 1.9Error messages:NOTE: available bundle cache has not been initialized yetmalloc(): unsorted double linked list corruptedAborted (core dumped) Any suggestions.Thank you.Jobi

4 8

Rotation using left mouse button
by y.v.hazendonk＠nki.nl 26 Feb '25

26 Feb '25

Hello, In my work with ChimeraX I have to rotate my proteins quite a lot to get a good look at different residues and helices. My problem is that very often when I am rotating my protein using the left mouse button, another piece of my protein will glide across my screen in the foreground, at which point the axis of rotation will lock onto this other piece. Is there a way to disable this unwanted locking? I am fine with these pieces floating across the foreground, as long as my axis of rotation doesn't suddenly lock onto them. I want the rotational axis to stay where it was when I started rotating. I look forward to your reply on how to fix this issue. Thank you in advance. With kind regards, Yorick van Hazendonk

5 6

Communicate between multiple ChimeraX instances
by Roden Deng Luo 25 Feb '25

25 Feb '25

Hi, I wonder if there is a way to synchronize two or more ChimeraX instances/sessions. For example, sync the camera. The meeting command ( https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/meeting.html) a great command I just got to know, is very close to what I am looking for. Only I will have different data in different instances, and toggles to enable and disable what features to be synced. If it is not currently implemented, how should I approach it as a developer? Many thanks, 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.

3 3

Measure angle between domains in chimeraX
by junjie han 24 Feb '25

24 Feb '25

Hi Elaine, I hope this email finds you well. May I ask how to measure the angle between two domains from one molecule or two different molecules in ChimeraX. Here are some examples below. Example 1: [cid:ee5ac0af-a9be-4e98-bb7c-e555c8f183c2] How to calculate these angles (54°, 38°)？ Example 2: [cid:24512415-5303-4be2-8f61-a4fd6acdc0ee] How to calculate this angle (75°) ? Example 3: [cid:f3ed355d-a961-4647-8a3c-b39ab3875cb8] How can I measure the rotation angle between A and B, or between two specific regions of these two molecules in ChimeraX? If I need to calculate the rotation angles of two molecules relative to a specific molecule, how can I define a shared axis for calculating the rotation angles? The rotation axes are different when I use the command “measure rotation A toModel B” to calculate the rotation angles, which is not an ideal way to compare them in parallel. Thank you in advance for your any suggestions. Very appreciated, Junjie

3 16

Trouble Morphing 2 Proteins
by Andrew Mejia Garnica 24 Feb '25

24 Feb '25

Hello, I have been using ChimeraX with a mac book from 2020 with a 1.1 GHz Dual-Core Intel Core i3, Intel Iris Plus Graphics 1536 MB and 8 GB of RAM. Everything seems to be working fine until I try to do a morph. Both proteins have been super positioned by matchmaker. I can only complete 5 frames out of the 60 with the command, morph #1,2 wrap true frames 60. However, I am not able to look through the frames, record or press play. I have tried it with the tutorial proteins as well and got stuck. The proteins that I am trying to morph will be attached to this email. I would like to ask if you could do a morphing for me or redirect me to be able to. I would also like to ask if it is a Graphis problem as I was also unsuccess full using a Dell laptop with a , 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHZ, 16GB of RAM, 64-bit operating system, x64-based processor. Thank you for your time and I hope to hear from you soon. Best, Andrew

2 5

Surface dust command in the .cxc script
by 李泽 24 Feb '25

24 Feb '25

Hi all: I'm trying to use the .cxc script to run the software, I found that the "surface dust" command has never been executed in it. Have anyone met the same problem? Any suggestions. Thank you all. Best, Ze

3 3

Freelance vs. Agency – Best Choice for Native App Developers Houston?
by hooria.khan＠algoace.com 23 Feb '25

23 Feb '25

I’m trying to decide whether I should hire a freelance developer or work with an agency for my native app development needs. Freelancers can be more affordable, but agencies offer structured project management. Are there any experienced <a href="https://algoace.com/houston-app-development/">Native App Developers Houston</a> who work independently and provide top-notch services? On the other hand, if you’ve worked with an agency, was the cost worth it? Any recommendations based on your experience?

1 0

Update chain description from fasta file
by Paul Sauer 23 Feb '25

23 Feb '25

Hi, I really like the 'sequence update' feature that was introduced in Chimerax 1.9. I was wondering if it is possible to expand the capability of this command to update the sequence description/ sequence name from the header line of an opened alignment or fasta file and write it out with the cif file. It seems like currently the full sequence is updated from an associated fasta file but the sequence names are being ignored. Could the sequence name written into the ' entity.pdbx_description' column in the resulting cif file? Or maybe there is already an option that I missed? Also, as a secondary feature request, maybe the sequence update command could not only write the ' entity_poly.pabx_seq_one_letter_code_can' table but also use the available coordinates and residue names of the structure to write the '_entity_ poly.pdbx_seq,_one_letter_ code' table for each polymer that includes modified residues/ligands etc in parentheses in addition to the canonical one letter code where known. I could imagine that these capabilities would make depositing coordinates of macromolecular complexes with many chains to the PDB much easier and more interactive, so maybe this would be helpful for other people as well. Thank you to the Chimerax team & contributors for creating such a great program, Paul

2 2

Dear ChimeraX users!
by amiraziznezhad＠gmail.com 23 Feb '25

23 Feb '25

Dear ChimeraX users! I am dealing with the analysis of protein-ligand interactions in a single PDB structure. I am looking for any tools implemented in Chimera-X, which could be used to analyse the interactions (besides the hbond and contact tools giving info in the log files msuic). I wonder to know which commands and corresponded ChimeraX tools could be used to produce the 2D contact diagrams shown on the Fig.4 as well as python graphs demonstrated on the Fig.5 in the Chimera-X article: https://www.myeasymusic.ir/ Many thanks in advance! Cheers Enrico

2 1

RspProp
by Robert Stanley 23 Feb '25

23 Feb '25

Hello - I was wondering what I have to do to install the RspProp tool? It doesn't appear in my utilities menu or the structure analysis one. I have version 1.9 (2024-12-11). I very much appreciate this program and use it in my Biochem and Biophysical Chemistry courses to expose the students to it ASAP. Thanks, Bob Stanley Robert J. Stanley, Ph.D. Professor of Chemistry 1901 N. 13th St., 250B Beury Hall Temple University Philadelphia, PA 19122 (215) 204-2027 https://www.cst.temple.edu/~rstanley/

3 2

Contribute to ChiemraX Recipe
by NG, Cheukhei Jackie [Student] 22 Feb '25

22 Feb '25

Dear ChimeraX Development Team, I am Jackie NG from a cryoEM group in the Hong Kong Polytechnic University interested in molecular visualization and analysis. I am writing to express my interest in contributing scripts to the ChimeraX library, specifically for inclusion in the ChimeraX Recipes. Sharing my scripts could benefit the community and enhance the utility of ChimeraX for various applications. The scripts are mainly quality-of-life improvements on copying selected parts of models, producing map-quality representations, organizing ligand chains, and many more. Please let me know if there is a process for submitting these scripts and any specific guidelines I should follow. I am eager to collaborate and contribute to the ongoing development of ChimeraX. Thank you for considering my contribution. I look forward to your response. Best regards, Jackie [https://www.polyu.edu.hk/emaildisclaimer/PolyU_Email_Signature-v2.jpg] Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.

2 2

Aligning fasta sequence with the sequence of pdb model in chimeraX
by Rayees Mattoo 21 Feb '25

21 Feb '25

Hi, I was wondering if there is a way in chimeraX to align fasta sequence with sequence from the loaded pdb model. Just wanted to be sure that the residue numbering matches the original Uniprot sequence. Any other suggestions that can do the job quickly are welcome. Best, Rayees

2 2

(no subject)
by FRANGIE Christian 21 Feb '25

21 Feb '25

Dear UCSF ChimeraX Support Team, My name is christian frangieh, I am currently using chimera x and i want to check the interacting residues that form the interface between 1 chain with 2 other different chains. for example my model has 3 chains (chain A,B,C) i want to have a list of the resideus of chain A and B that are interacting with chain C Can you please help me with this? Thank You

2 4

save clipped volume
by Yanhe Zhao 20 Feb '25

20 Feb '25

Greeting there ChimeraX developer and community, I have "clip" used on my map and currently want to save the clipped one as a new mrc file, what is the best way to do this? I checked the "save Map" command and found the region option, but I don't think it is the right option if I have my clip plan tilt. Thanks a lot for any input. Thanks and cheers, Yanhe

2 2

Help Needed with Building Capsid for ssRNA Homolog
by Bruno Hay Mele 20 Feb '25

20 Feb '25

Hi everyone, I am trying to build the capsid for a homolog of Chaetoceros socialis forma radians RNA virus 1 (PDB: 8b38). My approach was to work by homology, transferring the assembly/symmetry information from the PDB entry to my model, which I built by assembling homologs of the three subunits of 8b38. Unfortunately, this has not been as straightforward as I hoped. Ibm a complete newbie in this area, and my attempts to copy the relevant parts of the assembly information or use the ChimeraX bsymb tool have led nowhere. Could someone please point me to the right solution? Ibd really appreciate both: A practical solution: How to correctly transfer the symmetry information and generate the full capsid assembly in ChimeraX. Some references or explanations: Resources that explain why the solution works this way, so I can understand the underlying principles. Any help or pointers would be very much appreciated. Thank you very much for your time and assistance. Cheers, -- Bruno Hay Mele, PhD 2D-20, Biology Dept., University of Naples Federico II https://github.com/bhym/ | +39 081 67 9118

2 2

ChimeraX Model Joining
by Nieder, Claire 20 Feb '25

20 Feb '25

Hey there, I am a grad student at UConn trying to covalently link two PDB models by inserting a GFP into the third intracellular loop of 5HT4. If you have any advice, I would really appreciate it. Thanks, Claire Nieder Kienzler Lab UConn Chemistry

2 3

(no subject)
by FRANGIE Christian 20 Feb '25

20 Feb '25

Dear UCSF ChimeraX Support Team, My name is christian frangieh, I am currently using chimera x and i want to check the interacting residues that form the interface between 1 chain with 2 other different chains. for example my model has 3 chains (chain A,B,C) i want to have a list of the resideus of chain A and B that are interacting with chain C Can you please help me with this? Thank You christian

1 0

Re: [Chimera-users] script for clashes
by Eric Pettersen 18 Feb '25

18 Feb '25

Hi Valerio, Well, one of the main motivations for using ChimeraX is that running commands actually return results instead of nothing. So the 'clashes' command returns a dictionary of the clashes, as described here: https://github.com/RBVI/ChimeraX/blob/1bae62d955f4b9d6d05a31541af0372f11d36… . Therefore you do not need all that extra code that Chimera needs to try to determine if there were any clashes. Instead it's just: clashes = run(session, "clashes") if clashes: # code for existing clashes else: # code for no clashes Now, reasonable structures should have at most a few clashes, and usually zero, not many thousands like your structures seem to have. I suggest opening one of the structures interactively in ChimeraX, run the "clashes" commands and look to see why there so many clashes. --Eric > On Feb 17, 2025, at 3:03 AM, chiarini(a)takisbiotech.it wrote: > > Dear Prof Pettersen, > > Thank you so much for your advice. So far I managed to operate in chimeraX and now I can see the outputs of my script. righ now I'm running the following: > > > # -*- coding: utf-8 -*- > > import os > from chimerax.core.commands import run > > # Funzione principale che accetta la sessione > def process_pdb_files(session): > # Specifica la cartella con i file PDB > folder_path = "C:/Users/utente/Desktop" # Modifica il percorso della cartella > > # Stringa da cercare nei file > search_string = "A3a" > > # Lista dei file PDB nella cartella > file_names = [fn for fn in os.listdir(folder_path) if fn.endswith(".pdb")] > > # Stampa dei file trovati nella cartella per debugging > print("File trovati nella cartella:", file_names) > > # Loop su ogni file che contiene 'search_string' nel nome > for pdb_file in file_names: > if search_string in pdb_file: > pdb_path = os.path.join(folder_path, pdb_file) > > # Apre il file PDB > print(f"Apertura del file {pdb_file}...") > run(session, f"open {pdb_path}") > > # Calcola i clash (comando corretto per ChimeraX) > run(session, "clashes") > > # Verifica se ci sono clash > clashes_found = False > for m in session.models: > if getattr(m, 'category', None) == "contacts": > clashes_found = len(m.pseudoBonds) > 0 > if clashes_found: > break > > # Se ci sono clash, elimina il file > if clashes_found: > os.remove(pdb_path) > print(f"Clash trovati, il file {pdb_file} è stato eliminato.") > else: > print(f"Nessun clash trovato per {pdb_file}.") > > # Chiude il modello dopo averlo processato > run(session, "close all") > > # Questa parte assicura che la funzione venga chiamata correttamente > def main(session): > process_pdb_files(session) > > # Quando esegui lo script in ChimeraX, la sessione viene passata automaticamente > main(session) > > AND I GOT THE FOLLOWING OUTPUT: > > runscript C:/Users/utente/Desktop/chimera_script2.pyFile trovati nella cartella: ['A3a_structure_1.pdb', 'A3a_structure_2.pdb', 'A3a_structure_3.pdb', 'A3a_structure_4.pdb', 'A3a_structure_5.pdb'] > Apertura del file A3a_structure_1.pdb... > open C:/Users/utente/Desktop\A3a_structure_1.pdb > Chain information for A3a_structure_1.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes84336 clashes > Nessun clash trovato per A3a_structure_1.pdb. > close allApertura del file A3a_structure_2.pdb... > open C:/Users/utente/Desktop\A3a_structure_2.pdb > Chain information for A3a_structure_2.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes655434 clashes > Nessun clash trovato per A3a_structure_2.pdb. > close allApertura del file A3a_structure_3.pdb... > open C:/Users/utente/Desktop\A3a_structure_3.pdb > Chain information for A3a_structure_3.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes626886 clashes > Nessun clash trovato per A3a_structure_3.pdb. > close allApertura del file A3a_structure_4.pdb... > open C:/Users/utente/Desktop\A3a_structure_4.pdb > Chain information for A3a_structure_4.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes482406 clashes > Nessun clash trovato per A3a_structure_4.pdb. > close allApertura del file A3a_structure_5.pdb... > open C:/Users/utente/Desktop\A3a_structure_5.pdb > Chain information for A3a_structure_5.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes315894 clashes > Nessun clash trovato per A3a_structure_5.pdb. > close all > > > WHAT ELUDES ME IS THAT FOR EACH STRUCTURE CHIMERA FINDS LOT OF CLASHES BUT THEN RETURNS THE STATMENT "NO CLASH FOUND FOR STRUCTURE X". Why is that? I know these structures have lots of overlapping atoms and it also seems that chimera counts the class "clashes". But maybe it also includes contacts? > I would like to count only steric clashes and atoms superposition which makes the structure impossible. > Thanks in advance for your help. > > Best regards, > > Valerio Chiarini > > Il 2025-02-12 21:06 Eric Pettersen via Chimera-users ha scritto: >> Hi Valerio, >> I should preface things by saying that this script would be >> considerably easier to write in ChimeraX, because in ChimeraX the >> "runCommand" equivalent actually returns results from the command >> instead of nothing. So in ChimeraX you can directly determine if the >> clash-finding command actually found any clashes. >> So clearly the body of your 'if' statement never executed since it >> includes illegal statements that would have produced errors if the >> body of the 'if' statement had been executed, whereas you got no >> output. So the first thing is put "print file_names" right after the >> line that sets files_names and see if any of the file names contain >> your search string ("xxx"). If none of them do, then you need to >> figure out why: is folder_path wrong?; is search_string wrong?; do the >> files not end in .pdb?; etc. >> In addition, I can see some problems even if the 'if' statement body >> had executed. You don't close the models at the end, so they will >> build up and "findclash" will find more and more clashes. Your actual >> findclash command needs to be "findclash #0 test self". There is no >> "chimera.clashClashList". Probably the simplest way to determine if >> clashes were found is checking if the clashes pseudobond group has any >> pseudobonds in it. You can do that with: >> for m in chimera.openModels.list(hidden=True): >> if getattr(m, 'category', None) == "contacts": >> clashes_found = len(m.pseudoBonds) > 0 >> break >> --Eric >> Eric Pettersen >> UCSF Computer Graphics Lab >>> On Feb 12, 2025, at 2:23 AM, valerio chiarini via Chimera-users >>> <chimera-users(a)cgl.ucsf.edu> wrote: >>> Dear Responsible, >>> I am working on a script that should iterate through several >>> structures, check the structures for clashes among all atoms, and >>> eliminate the pdb in any clashes are found. >>> Here is what I have worked out so far: >>> # -*- coding: utf-8 -*- >>> import os >>> from chimera import runCommand as rc >>> from chimera import replyobj >>> import chimera >>> # Specify folder >>> folder_path = "/gporq3/store_0/usr/chiarini/chroma/chroma/" >>> # String to be found >>> search_string = "xxx" >>> # List of files in the folder >>> file_names = [fn for fn in os.listdir(folder_path) if >>> fn.endswith(".pdb")] >>> print("File trovati nella cartella:" + str(file_names)) >>> # Loop on every file containing 'search_string' in the name >>> for pdb_file in file_names: >>> if search_string in pdb_file: >>> pdb_path = os.path.join(folder_path, pdb_file) >>> # Open the PDB >>> rc("open {}".format(pdb_path)) >>> # Calculates clashes >>> rc("findclash") >>> rc("wait") >>> # Verify if any clashes are found >>> clashes = chimera.clashClashList() >>> if clashes: >>> # If clashes are found eliminates the file >>> os.remove(pdb_path) >>> print("Clash trovati, il file {} è stato >>> eliminato.".format(pdb_file)) >>> else: >>> # If no clash, exit normally >>> print("Nessun clash trovato per {}.".format(pdb_file)) >>> But no analisys is done at all. I have been searching through the >>> script page (https://www.rbvi.ucsf.edu/trac/chimera/wiki/Scripts) in >>> order to found some clue on this function but so far I have found >>> none. >>> Could you help me on this issue? >>> Thank you in advance >>> Valerio Chiarini _______________________________________________ >>> Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu >>> To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu >>> Archives: >> https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/ >> _______________________________________________ >> Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu >> To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/ > > -- > Dr. Valerio Chiarini > > _Senior Scientist_ > > Proteins & Monoclona Antibodies Department – Takis Biotech > > c/o Tecnopolo > > Via di Castel Romano, 100 > > 00128 Rome, Italy > > Tel.: +39 06-50576077 > > Fax: +39 06-50576710 > > Email: chiarini(a)takisbiotech.it > > Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.takisbiotech.it&d=D… > > D_.lgs. 196/03_ > > _Le informazioni contenute in questa comunicazione e gli eventuali > documenti allegati hanno carattere confidenziale, sono tutelate dal segreto > professionale e sono ad uso esclusivo del destinatario. Nel caso questa > comunicazione Vi sia pervenuta per errore, Vi informiamo che la sua > diffusione e riproduzione è contraria alla legge e preghiamo di darci > prontamente avviso e di cancellare quanto ricevuto. __Grazie._ > > _This e-mail message and any files transmitted with it are subject to > attorney-client privilege and contain confidential information intended > only for the person(s) to whom it is addressed. If you are not the intended > recipient, you are hereby notified that any use or distribution of this > e-mail is strictly prohibited: please notify the sender and delete the > original message. __Thank you._ >

1 0

Bundle development for chimeraX - svg onClick event to run command from QWebEngineView
by Lou Holland 18 Feb '25

18 Feb '25

Hello, Apologies if this is the wrong email address to contact about this. I am currently working on a privateer bundle for carbohydrate validation in chimeraX. At present, I have it so that the privateer tool will display SNFGs of glycans present in the structure using svgs displayed in a QWebEngineView(). I would like, if possible, on clicking elements of the svg to run a chimeraX command (view /chainID:resID) to centre the view window on the residue in question. At present, I can implement an onClick event to display the command that should be run, but haven't managed to figure out how to just run the command from within that QWebEngineView. Is there a mechanism already in place for doing something like this that I could take advantage of? I'd considered using the "log html" to display the svgs in the log instead of the WebEngineView() so that I could take advantage of the href="cxcmd" functionality, but the svgs are long, with semicolons and new-line characters which interfere with this. Best wishes, Lou Holland (Pronouns: they/them) Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK

3 3

Assistance with ChimeraX Syntax for SPRITE Hands-On Module
by Zeenat Bashir 18 Feb '25

18 Feb '25

Dear ChimeraX Developers, I hope this email finds you well! I am currently developing a hands-on module for my students on visualizing SPRITE results using ChimeraX. However, I am facing an issue with the syntax for aligning the residues of *2HNT* with *1A0J*. The module I am using, which was provided by Basil (attached with this email), includes syntax for Chimera (refer to Figures 10 and 11 in the attached document). I have tried adapting the syntax for ChimeraX but have not been successful. I would really appreciate your guidance on this matter or if you could direct me to someone who might be able to assist in generating the correct command line syntax. Thank you so much for your time and help! 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

2 1

Roll command for multi objects in grid
by Enrico Martinez 18 Feb '25

18 Feb '25

Dear ChimeraX users! Using til command I split six superimposed structures, displaying them as the 2x3 table and then rotate each object along its axis within each grid using "roll" in the following way: # for 6 different object roll models #1 center #1 & protein roll models #2 center #2 & protein roll models #3 center #3 & protein roll models #4 center #4 & protein roll models #5 center #5 & protein roll models #6 center #6 & protein Would it be possible to simplify this to one "roll" command that will automatically rotate all displayed objects in the separate grids along its axis ? Many thanks in advance Enrico

2 3

Questions about match and view commands
by Enrico Martinez 16 Feb '25

16 Feb '25

Dear ChimeraX users! I am performing a visualization of the ensemble of conformers for the same protein defined in the chimerax as models #1 to #6. Here are some of my questions: 1 - I try to superimpose all structures to the first model using match #2-5 to #1 is it possible to use some regular expression instead of #2-5 to select all models from the second to the last e.g. to superimpose all structures to the first one in the script. 2 - I try to automatically orient the superimposed models along its principal axe in one command e.g. using view orient but it does not produce a proper orientation. What kind of trick could work for a nanobody object to orient it automatically e,g, along Z ? Many thanks in advance Enrico

3 6

assistance on bundle writting
by Nguyen, Catherine 14 Feb '25

14 Feb '25

Hello, I was hoping to get your help. I am trying to write a bundle and I am struggling to figure out how I can add psuedo-bonds using python as I want to connect two amino acids by the CA. Would you be able to help me find a way to do this? I hope to hear from you soon, Best wishes, Catherine

2 6

MUNKI Managed Software Download URL
by Antony Nelson 14 Feb '25

14 Feb '25

Hi, I appreciate this might seem an odd request, but do you have a public download location for ChimeraX software? There exists a widely used system by which administrators of Apple computers distribute software to their users by means of applications known as Munki and Autopkgr. Software which can be downloaded from public websites can be managed in such a way that new releases and updates are automatically added to the software repository Apple administrators curate for their users. Without making this publicly available, admins will only update your software when users request the admins to do so. Looking back on the Loupe Browser instances that have been made available to my users, they have only had access to versions: 0.8.0 0.9.0 0.9.1 0.93.0 1.1.1 1.7.1 and today they will have 1.9.0 If your software was made available via public download by a predictable URL, then they would have had access to every version released on the day it was added to your website since it was first requested by users. If you are concerned about the acceptance of terms of conditions then perhaps this could be incorporated into the URL string. Regards

2 1

How to get different silhouette widths for 2 maps
by Hong ZHAN 13 Feb '25

13 Feb '25

Hi there, I am trying to create a video with two maps overlay with different silhouette widths. It is easy to do with 2 images, but how I can do it in a video setting? If I change the width to 6, all maps changes the width to 6. Thanks! -Hong

3 4

Unable to load scripts at startup
by Pranav Shah 13 Feb '25

13 Feb '25

Hi Team, (I accidentally sent this to ChimeraX-bugs, copying it again here) I am trying to load some scripts at startup via the chimerax_custom_functions.cxc command file - open /Users/ps/.chimerax/chimerax_commands/chimerax_custom_functions.cxc in the log file I see the following message: still retrieving bundle list from toolshed open /Users/ps/.chimerax/chimerax_commands/chimerax_molmap_cube.py Error running startup command 'open /Users/ps/.chimerax/chimerax_commands/chimerax_custom_functions.cxc': Unknown command: open /Users/ps/.chimerax/chimerax_commands/chimerax_molmap_cube.py This is strange as simply running "open /Users/ps/.chimerax/chimerax_commands/chimerax_molmap_cube.py" in the ChimeraX command panel runs perfectly fine! the error occurs only when I try to run that line through the .cxc file. Am I missing something? or could this be a bug? I am on the stable release of ChimeraX (version 1.9). Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

3 3

PAEcontacts colorkey
by ccinsua＠gmail.com 13 Feb '25

13 Feb '25

Hi all, Thank you very much for your work with chimerax. I've been using it to study alphafold complex prediction, and I find the command alphafold contacts very useful. The default color key (guess it is paecontacts, according to documentation) ranges are blue (low PAE) - green (medium PAE) - yellow (high PAE). However, I am unable to add a color key using "key paecontacts". Somehow I have to define it myself. Is there anything I am missing? I would like to stick to the blue-green-yellow scheme. Thanks a lot in advance Carlos

1 1

NASA - Country of Origin Statement and 508 Conformance Request: UCSF ChimeraX
by Price, Dru C. (LARC-B730)[eMITS] 12 Feb '25

12 Feb '25

Hello, my name is Dru and I work for the NASA Commercial IT Acquisition Team. As such, I ensure that all NASA acquisitions of Covered Articles comply with Title II; General Provision Section 208 and Title V; General Provisions Section 514 of the Consolidated Appropriations Act, 2021, Public Law 116-260<https://www.congress.gov/bill/116th-congress/house-bill/133/text>, enacted December 27, 2020. To do so, the Country of Origin (CoO) information must be obtained from the company that develops, produces, manufactures, or assembles the product(s). Please specifically identify the country, or countries, in which each of the following software products is developed and maintained: * UCSF ChimeraX Additionally, if available, please identify all authorized resellers of the product(s) in question. Finally, I am requesting an Accessibility Conformance Report (starting from Page 10 of the attached VPAT) be completed and returned so that NASA can assess the product's level of 508 Conformance. More information regarding Section 508 of the Rehabilitation Act of 1973 and what it means to manufacturers/developers can be found at https://www.section508.gov/sell/vpat. I have attached a blank copy of the latest revision of the VPAT standard if you do not already have a completed VPAT available for this product. Please complete this document to the best of your abilities, if one is not already available. Product / Service Description Model Number Country of Origin Is final testing performed in the United States? Please let me know if you have any questions. Thank you, Dru C. Price Procurement Analyst eMITS | [ROTHE ARES JV] Commercial IT Management Support Croscutting Agency Service (CAS) Branch Enterprise Business Management Office (EBMO) NASA - Office of the Chief Information Office (OCIO) [cid:image001.png@01DB7D5D.40BD4D20]<https://teams.microsoft.com/l/chat/0/0?users=dru.c.price@nasa.gov> [cid:image002.png@01DB7D5D.40BD4D20]

3 3

ChimeraX fetch by PubChem CID
by Elaine Meng 12 Feb '25

12 Feb '25

> On Feb 12, 2025, at 11:41 AM, Alexander Mansueto <alexander.j.mansueto(a)vanderbilt.edu> wrote: > > Can we import pubchem CID molecules to model proteins with lipids? Would be very cool. Hi Alexander, The recommended address for asking ChimeraX questions is the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> mailing list CC'd here, see "contact us" on our website or in the ChimeraX menu: <https://rbvi.ucsf.edu/chimerax/docs/contact.html> If PubChem Compound has the coordinates, you can open them in ChimeraX by CID, e.g. command open pubchem:12123 - OR - open 12123 from pubchem ... as explained here <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> ...or with menu: File... Fetch by ID, choosing the Pubchem option and specifying the CID in the dialog: <https://rbvi.ucsf.edu/chimerax/docs/user/fetch.html> However, not every entry in PubChem Compound has coordinates available, so I don't know if it will work for your specific molecules of interest. 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

Get color code of a custom color
by Ahmad Khalifa 11 Feb '25

11 Feb '25

I created a custom color that I want to use in a different session. is there a way to do that besides trying to match colors by eye? Regards.

5 4

steam VR running but still get an error with Vr on command.
by Krishnan Raman 10 Feb '25

10 Feb '25

[cid:5bbc0381-58d6-4058-bc7c-183bcd144645] Steam VR is running and still i get this error. Am i overlooking something? thanks Krish CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

2 1

there is no amination？？？
by 刘涛 07 Feb '25

07 Feb '25

2 2

Recording MD Trajectory Movie in ChimeraX
by Gourav Das 07 Feb '25

07 Feb '25

Dear ChimeraX users, I have performed MD simulation of a system using AMBER20. The topology and trajectory files are in .parm7 and .nc formats, respectively. I would appreciate your guidance on visualizing and recording the trajectory as a movie in ChimeraX. Thank you for your support. With regards, Gourav Das Research Scholar Department of Chemistry Indian Institute of Technology Kharagpur West Bengal, India-721302 Mob: +91-6295251060 --

2 5

Double and Triple Bond Stick Style
by Smith, Chase 05 Feb '25

05 Feb '25

Dear ChimeraX, I was just wondering why there is no way to represent a double or triple bond in either the ligands or the protein amino acids when viewing as a Stick or Ball-and-Stick representation? I sometimes use Chimera or ChimeraX to make visuals for my lectures, and the students often have difficulty in understanding due to the absence of the multiple bonds. I would love to have the ability to represent the double or triple bonds with multiple lines between the atoms. Thank you, Chase Smith ... ChaseSmith, PhD Chair, Department of Pharmaceutical Sciences & Associate Professor of Medicinal Chemistry School of Pharmacy MCPHS University 19 Foster Street | WorcesterMA01608 T 508.373.5717F 508.890.5618C 978.855.7203 chase.smith(a)mcphs.edu www.mcphs.edu MCPHS University Confidentiality Note: This e-mail, and any attachment to it, is intended to be confidential and might be legally privileged. It is intended solely for the use of the addressee. If you are not the intended recipient, you are hereby notified that reading, copying, disseminating or distributing this email is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.

5 5

Re: Introduction of a proteolytic cleavage in ChimeraX
by Elaine Meng 04 Feb '25

04 Feb '25

> On Feb 4, 2025, at 3:30 AM, Mark Hilge <markhilge(a)icloud.com> wrote: > > Dear Dr. Meng, > [... details removed ...] > Question: In ChimeraX, is there a possibility to introduce a proteolytic cleavage between say Leu112 and R113? This should result in Leu112 with a carboxylate group followed by a TER keyword. > > Many thanks in advance! > Kind regards, > Mark Dear Mark, It depends what you want to use this for. If it's just for a figure, that is totally different than if you were going to do some extensive workflow afterwards. If you have an input PDB file, one "dumb" way is to text-edit it to put the TER card in before opening in ChimeraX. However, that will not add a carboxylate oxygen, there would just be a dangling C=O. If you wanted an OXT you would have to add it "manually," e.g. in the Build Structure tool. However, that will be problematic because it won't want to add the OXT right on top of the N, which is where it would want to go. You'd also have to change the conformation of the chain, e.g. rotate a bond with the mouse mode or the "torsion" command. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html> Within ChimeraX, you could use command ~bond to remove bonds. However, if you do this within a chain defined in the input (e.g. PDB SEQRES lines or mmCIF file equivalent), it will then draw a dashed line because it still "knows" they are supposed to be connected within the chain because of the SEQRES records in the PDB file. <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html> So it's all more complicated than you might think, especially if you wanted everything to be correct for some subsequent modeling workflow. You might instead give the two parts two different chain IDs. One way is to text-edit the PDB file. Another is to open the thing twice, delete the first part of the chain in one copy, delete the other part of the chain in the other copy, and then use "combine" to create a new model that has both parts but with different chain IDs, and then use "save" to save a PDB file of that combined model. <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> However, you would still need to text-edit the PDB file manually so that there are SEQRES records for the two different chains (the two parts of the original single chain) that each contain only the residues for the corresponding part. These are different than the ATOM records that have the coordinates. And I can't even begin to explain how you might do it in mmCIF, all of this is in PDB format only. So if you bothered to do all that, then if you use "addh" it will automatically add the "OXT" because it will finally recognize the new cleaved C-terminus as a real C-terminus. <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/addh.html> For future reference: please use chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address CC'd here to ask questions about ChimeraX, omitting any information that needs to remain private. If you send email to me only, it may not get answered. Thanks, 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

2 1

Suppress errors when using runscript?
by Vorländer,Matthias Kopano 03 Feb '25

03 Feb '25

Hi, I wondered if it is possible to suppress/ignore an error message when executing scripts with runscript. Specifically, I have a script to analyze alphafold (3) predictions and select residue interfaces residues using the interface select command. The selection for each of the five model is then saved in a named selection: # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection for the interface residues. name frozen interface_residues$2_model_4 sel This works fine when all models show contacts , however, if one of the models/predictions does not have any residues involved in an interface, the script stops with the error “Nothing is selected by the specifier”. It would be great if the script does not pause at this message. Below the full .cxc script I am using: Best, Matthias # Generate AF contacts for all predictions of an AF3 run # # Usage: # runscript analyse_af3_prediction.cxc <AF_screen_directory> <custom_prediction_name> # The script assumes that five models were generated by AF. It expects the CIF files to be in a sub‐directory # matching the pattern "*model_X*.cif" and the corresponding JSON files in a sub‐directory matching "*data_X*.json" # for each model number X (4, 3, 2, 1, 0). # For the alignment and mseries slider command to work properly, the script assumes no other models are open. echo "Usage: runscript analyse_af3_prediction.cxc <AF_screen_directory> <custom_prediction_name>" ##### Model 4 ##### # Open the structure and its JSON scores for model 4. open $1/*model_4*.cif open $1/*data_4*.json structure last-opened hide show c # Generate AF contacts (using JSON scores) for chain A (or the first chain) alphafold contacts last-opened &/A name model_4_af_contacts_$2 # Create pseudobonds for the contacts and label them with residue names and numbers. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Save the pseudobond representation to a file. save $1/af_contacts_model_4_$2.txt format pseudobonds sel true echo "AlphaFold contacts (derived from JSON file) saved to $1/af_contacts_model_4_$2.txt" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection for the interface residues. name frozen interface_residues$2_model_4 sel show interface_residues$2_model_4 style interface_residues$2_model_4 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_4 saveFile $1/interface_residues$2_model_4_buriedArea_300.txt # Color the model for clarity. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_4 and info saved to $1/interface_residues$2_model_4_buriedArea_300.txt" ##### Model 3 ##### # Open the structure and its JSON scores for model 3. open $1/*model_3*.cif open $1/*data_3*.json structure last-opened hide show c # Generate AF contacts. alphafold contacts last-opened &/A # Create pseudobonds and label them. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Save the pseudobond representation. save $1/af_contacts_model_3_$2.txt format pseudobonds sel true echo "AlphaFold contacts (derived from JSON file) saved to $1/af_contacts_model_3_$2.txt" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection. name frozen interface_residues$2_model_3 sel show interface_residues$2_model_3 style interface_residues$2_model_3 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_3 saveFile $1/interface_residues$2_model_3_buriedArea_300.txt # Color the model. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_3 and info saved to $1/interface_residues$2_model_3_buriedArea_300.txt" ##### Model 2 ##### # Open the structure and its JSON scores for model 2. open $1/*model_2*.cif open $1/*data_2*.json structure last-opened hide show c # Generate AF contacts. alphafold contacts last-opened &/A # Create pseudobonds and label them. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Save the pseudobond representation. save $1/af_contacts_model_2_$2.txt format pseudobonds sel true echo "AlphaFold contacts (derived from JSON file) saved to $1/af_contacts_model_2_$2.txt" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection. name frozen interface_residues$2_model_2 sel show interface_residues$2_model_2 style interface_residues$2_model_2 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_2 saveFile $1/interface_residues$2_model_2_buriedArea_300.txt # Color the model. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_2 and info saved to $1/interface_residues$2_model_2_buriedArea_300.txt" ##### Model 1 ##### # Open the structure and its JSON scores for model 1. open $1/*model_1*.cif open $1/*data_1*.json structure last-opened hide show c # Generate AF contacts. alphafold contacts last-opened &/A # Create pseudobonds and label them. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection. name frozen interface_residues$2_model_1 sel show interface_residues$2_model_1 style interface_residues$2_model_1 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_1 saveFile $1/interface_residues$2_model_1_buriedArea_300.txt # Color the model. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_1 and info saved to $1/interface_residues$2_model_1_buriedArea_300.txt" ##### Model 0 ##### # Open the structure and its JSON scores for model 0. open $1/*model_0*.cif open $1/*data_0*.json structure last-opened hide show c # Generate AF contacts. alphafold contacts last-opened &/A # Create pseudobonds and label them. sel last-opened&pbonds label sel pseudobonds text "{0.atoms[0].residue.name} {0.atoms[0].residue.number} to {0.atoms[1].residue.name} {0.atoms[1].residue.number}" # Save the pseudobond representation. save $1/af_contacts_model_0_$2.txt format pseudobonds sel true echo "AlphaFold contacts (derived from JSON file) saved to $1/af_contacts_model_0_$2.txt" # Select interface residues using the interfaces command. interfaces select last-opened&/A contacting last-opened&~/A bothSides true # Create a named selection. name frozen interface_residues$2_model_0 sel show interface_residues$2_model_0 style interface_residues$2_model_0 ball # Save interface residue info to a file in the input directory. info residues interface_residues$2_model_0 saveFile $1/interface_residues$2_model_0_buriedArea_300.txt # Color the model. rainbow last-opened chains palette bupu color byhetero echo "Interface residues saved in named selection interface_residues$2_model_0 and info saved to $1/interface_residues$2_model_0_buriedArea_300.txt" ##### Final Steps ##### # Move all models (except the last-opened) to a common group (optional) mm #*&~last-opened&/A to last-opened&/A # Create an mseries slider for the five models. mseries slider #1-5 title $2 name $2_slider mseries #1-5 echo "Use the slider to go through the models!" echo "Pairwise contacts (based on the JSON fle) and all residues involved in an interface (based on a buried surface are of 300 Angstrom or more) have been saved in the input folder for each prediction" echo "You might want to increase stringency by calcualting the overlap between all predictions"

2 1

Getting two color keys in the same ChimeraX session
by Elaine Meng 03 Feb '25

03 Feb '25

> Begin forwarded message: > > From: Eric Pettersen via Chimera-users <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] Re: key command > Date: February 3, 2025 at 11:52:12 AM PST > To: Fabian Glaser <fglaser(a)technion.ac.il> > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Reply-To: chimera-users(a)cgl.ucsf.edu, Eric Pettersen <pett(a)cgl.ucsf.edu> > > Hi Fabian, > There is no direct support for multiple keys, but it is pretty easy to “trick” ChimeraX into showing multiple keys. You would create your first key normally, getting it exactly the way you want it to look before creating the next key. You create the next key with the following Python code: > > from chimerax.color_key.model import ColorKeyModel > m = ColorKeyModel(session) > > If the above was in a file ending in ‘.py’, you could just use the ‘open’ command to run it and create the key. I’ve attached a file with that code in it for convenience. Once you have created the key, then all operations that affects keys (like the ‘key’ command) will affect the new key and leave the original key as is. If you had the Color Key tool up, it will continue to show the old values. Just close it and re-open it to show the new values. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > >> On Feb 3, 2025, at 6:31 AM, Fabian Glaser via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >> >> Hi, >> >> We would be interested to add more than one key color bar in the same chimerax session. But we noticed the key command allows only one color key can be present at a time. >> >> Is there a way to add more than one color key in the same session? >> >> Thanks a lot, >> >> Fabian >> >> >> Fabian Glaser, PhD >> >> Technion Centre for Structural Biology (TCSB), Computational Section, Head >> Technion Human Health Initiative (THHI) >> Technion - Israel Institute of Technology, Haifa, Israel >> fglaser(a)technion.ac.il >> +972 (0)48293701 >> >> >> >> _______________________________________________ >> Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu >> To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/ > > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

1 0

Grid mode and multiple viewports
by Roden Deng Luo 03 Feb '25

03 Feb '25

Hi, I find there is a `tile` command. After I enter the tile mode, the zoom is global. I guess `tile` is implemented by transforming the active models in the global scene explicitly. I wonder if there is a way to have the zoom independent for each model, similar to the grid mode in PyMol. A further question, more from a developer's perspective, is whether having multiple 3D rendering viewports in ChimeraX is possible. I imagine each viewport can have its own active models in the scene and its own camera. Different cameras and other operations might be synced upon users' request. This video (https://youtu.be/7KZ1P-nPav8?si=Z1hiBBuRiWop2WFC) demos the feature (in an old version of Houdini). Thanks, 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.

4 8

aligning maps generated by chimeraX
by msteves＠berkeley.edu 31 Jan '25

31 Jan '25

Hello, I'm new to Chimera, but would like to use it to generate surface maps of electrostatic potential and hydrophobicity, then output for further analysis. I've generated maps using coulombic and mlp commands, and successfully saved these to .MRC format. However, when I go and read these files, the dimensions of the maps are different, so I'm not sure how to properly overlay these maps in my later analysis. Is there a way to have Chimera generate maps only within a given spatial range, so I end up with maps of the same size? Or another way you would recommend going about this? In later analysis I'd also like to make use of the SAS calculated by Chimera, and I imagine I will also have difficulties properly aligning the surface to the maps, so any advice on this would also be greatly appreciated! Thanks, Megan Steves

2 1

Question about Surface Volume Overlap Calculation
by John Watters 31 Jan '25

31 Jan '25

Hello, I was wondering if anyone had any tips/tricks/useful functions for quantifying the volume of the overlap between two surfaces in ChimeraX? I am looking specifically to make a metric to compare steric clashes of molecules in different orientations. Thank you for any help you can provide! Best, John

3 4

Add help for reusable ChimeraX script that takes command line arguments?
by Vorländer,Matthias Kopano 30 Jan '25

30 Jan '25

Hi, It’s me again 😉 I wondered how I can add a help page to a re-usable ChimeraX script that is run via runscript. I saved the following script in my ChimeraX presets: #Required arguments: first is the uniprot ID, second is the model ID that will be used for mapping! alphafold fetch $1 #get the missense data open $1 fromDatabase alpha_missense format amiss #associate missense data to structure mutationscores structure $2 #label each residue with matric mutationscores label #1 amiss height 3 #define a new score called avg by avergaing over all substitution scores mutationscores define avg fromScore amiss setAttribute true combine mean #color by avg missense score color byattribute r:avg $2 target csab palette palette bluered range full #scale cartoon by acg missense score cartoon byattribute r:avg #!$2 and then defined an alias in my startup commands so I don’t need to type the full path alias map_missense runscript /Users/matthias.vorlaender/Documents/ChimeraX_presets/map_missense.cxc $1 $2 Is there a way to display the expected user inputs when the script is called without arguments? Cheers, Matthias

2 3

Feasibility of selecting chain ID via uniprot ID?
by Vorländer,Matthias Kopano 30 Jan '25

30 Jan '25

Hi again : ) When comparing structures from different sources (such as different PDB depositions, or an Alphafold structure), it is always tedious to figure out which chain belongs to which protein (especially for large structures like spliceosomes) for consistent coloring or alignment. I wondered if it would be technically feasible to use the uniport ID to match a specific chain directly, since the association between chain ID and uniport ID should be present at least in structures from curated databases such as the PDB and Alphafold. So the ambition would be to be able to use ‘color IF4A3_HUMAN red’ directly, without having to look chain IDs. An added bonus would be to be able to skip the species identifier, in case you have models containing IF4A3_MOUSE and IF4A3_HUMAN, and match both with IF4A3 …. Would be curious to hear your thoughts. Thanks a lot, and best wishes, Matthias

3 3

Encode: saving a movie on a Windows laptop, and colouring residues in the multiple sequence
by Anne-Frances Miller 30 Jan '25

30 Jan '25

Dear ChimeraX My class is having a blast with this! I have assigned the class to make a movie, based on the morph and encode commands. On Macs, your instructions are flawless. However I have students using Windows10 and Windows 11. For these, could you please provide an example movie encode command including path and good choice of format please? Also, when I open a multiple sequence alignment in ChimeraX, is there a way to apply Taylor or other colouring to the MSA? This used to be possible in Chimera's MAV. Thank you, Anne-Frances Novel Meritorious Research (and teaching) —•—•—•—•—•—•—•—•—•—•—•—•—•— A.-F. Miller, Ph. D. (she/elle/sie) Distinguished Prof. of Arts and Sciences Professor of Chemistry University of Kentucky https://uky.zoom.us/j/3250841836 https://millerlablive.wordpress.com/ Visiting Fellow, Einstein Foundation of Berlin

3 4

Possible to plot attribute value over sequence?
by Vorländer,Matthias Kopano 29 Jan '25

29 Jan '25

Dear ChimeraX team, I wondered if it is possible to generate a line or scatter plot of an attribute value (B factor, Alphafold pLDDT scores, or AlphafoldMissense score…) over the residue number? For example something like this (taken from https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0089116) : [cid:image001.png@01DB7242.B1C3F8A0] Specifically, for the AlphafoldMissense data, such a plot would be more informative then the default histogram that is displayed when fetching the scores when looking for functional hotspots in your POI. Many thanks, MAtthias

3 5

Chai discovery data
by Reza Salavati, Prof. 29 Jan '25

29 Jan '25

Hello, I have downloaded the Chai discovery data in .npy and .json file formats. How can I open these files in Chimera X? Thank you Reza

4 4

ChimeraX installation on Debian Trixie? (Unsatisfied dependencies)
by Francisco Murphy Pérez 29 Jan '25

29 Jan '25

``` root@debian# apt install ./ucsf-chimerax_1.9ubuntu24.04_amd64.deb Note, selecting 'ucsf-chimerax' instead of './ucsf-chimerax_1.9ubuntu24.04_amd64.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: Unsatisfied dependencies: ucsf-chimerax : Depends: libgdk-pixbuf2.0-0 but it is not installable root@debian# apt install ./libgdk-pixbuf-2.0-0_2.42.12+dfsg-1+b1_amd64.deb Note, selecting 'libgdk-pixbuf-2.0-0' instead of './libgdk-pixbuf-2.0-0_2.42.12+dfsg-1+b1_amd64.deb' libgdk-pixbuf-2.0-0 is already the newest version (2.42.12+dfsg-1+b1). libgdk-pixbuf-2.0-0 set to manually installed. Summary: Upgrading: 0, Installing: 0, Removing: 0, Not Upgrading: 0 ``` From here https://github.com/RBVI/ChimeraX/blob/develop/mkubuntu.py (line 308) looks like "libgdk-pixbuf2.0-0": "2.40.0+dfsg", is missing a dash?

2 1

Re: [Chimera-users] How to subgroup the chains of oligomer pdb
by Elaine Meng 28 Jan '25

28 Jan '25

Hello, If you are asking about ChimeraX, it is better to use the address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here, instead of the older Chimera address. I don't know if this is exactly what you want but you can give a name to any set of atoms. For example, open your-oligomer.pdb name frozen mygroup1 #1/A-F name frozen mygroup2 #1/G-L select mygroup1 color mygroup2 orange See ChimeraX "name" command (your name can be something else, like gp20 instead of mygroup1): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html> Or, a totally different thing you could do is split the model into two different models, for example, open your-oligomer.pdb split atoms #1/A-F atoms #1/G-L That would make your model #1 into two separate models #1.1 and #1.2 with the specified sets of atoms. See ChimeraX "split" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html> You can also change names of models (what is shown in the Models list) using the "rename" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.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 > On Jan 24, 2025, at 8:14 PM, sktewary via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Friends > > I would like to learn how to subgroup the chains of a oligomer pdb. suppose i have a pdb with chain A to L, in which A,B,C,D,E,F belongs to gp20 and G,H,I,J,K,L belongs to gp20. My question is how to add the descriptions to these groups chains so that when the viewer look the pdb file when he selects the gp20 all the chains to this group are selected A-F. > > Please give your feedback if chimerax can do it, how to do it?

2 1

Limit blast search to species
by Vorländer,Matthias Kopano 28 Jan '25

28 Jan '25

Dear ChimeraX team, I wondered if it is possible to limit a BLAST search to only a single species when querying a selected database. This would facilitate identifying homologs in your favorite model organism, rather than picking up the most closely related homolog overall (i.e when using the alphafold database). Many thanks, Matthias

3 7

Clustal alignment
by Rosaleen Calvert 28 Jan '25

28 Jan '25

Hi. Apparently alignment is newly available in Chimerax 1.9. I cannot find how to do this in Tools: sequence or Tools: structure analysis. From Rosy Calvert

2 1

movie crossfade
by Enrico Martinez 27 Jan '25

27 Jan '25

Dear ChimeraX users! I am recording a short animation demonstrating my docking ensemble # start recording movie record ## play DOCKING movie from end to begining coordset #1 96,1,-1 wait 96 Would it be possible to add a smooth transition between each frame (docking pose) using the movie crossfade command ? If so, how should this command be placed in the script ? Many thanks in advance ! Enrico

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Fwd: ChimeraX installation on Debian Trixie? (Unsatisfied dependencies)
by Eric Pettersen 27 Jan '25

27 Jan '25

Greg, I’m guessing this is yours… —Eric > Begin forwarded message: > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Fwd: [chimerax-users] ChimeraX installation on Debian Trixie? (Unsatisfied dependencies) > Date: January 23, 2025 at 3:45:29 PM PST > To: chimerax-programmers(a)cgl.ucsf.edu > Cc: Elaine Meng <meng(a)cgl.ucsf.edu> > > Anybody? > >> Begin forwarded message: >> >> From: Francisco Murphy Pérez via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> >> Subject: [chimerax-users] ChimeraX installation on Debian Trixie? (Unsatisfied dependencies) >> Date: January 19, 2025 at 1:22:00 PM PST >> To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> >> Reply-To: Francisco Murphy Pérez <francisco.murphy(a)ibt.unam.mx> >> >> ``` >> root@debian# apt install ./ucsf-chimerax_1.9ubuntu24.04_amd64.deb >> Note, selecting 'ucsf-chimerax' instead of './ucsf-chimerax_1.9ubuntu24.04_amd64.deb' >> Some packages could not be installed. This may mean that you have >> requested an impossible situation or if you are using the unstable >> distribution that some required packages have not yet been created >> or been moved out of Incoming. >> The following information may help to resolve the situation: >> >> Unsatisfied dependencies: >> ucsf-chimerax : Depends: libgdk-pixbuf2.0-0 but it is not installable >> >> root@debian# apt install ./libgdk-pixbuf-2.0-0_2.42.12+dfsg-1+b1_amd64.deb >> Note, selecting 'libgdk-pixbuf-2.0-0' instead of './libgdk-pixbuf-2.0-0_2.42.12+dfsg-1+b1_amd64.deb' >> libgdk-pixbuf-2.0-0 is already the newest version (2.42.12+dfsg-1+b1). >> libgdk-pixbuf-2.0-0 set to manually installed. >> Summary: >> Upgrading: 0, Installing: 0, Removing: 0, Not Upgrading: 0 >> ``` >> >> From here https://github.com/RBVI/ChimeraX/blob/develop/mkubuntu.py (line 308) looks like "libgdk-pixbuf2.0-0": "2.40.0+dfsg", is missing a dash? >> >> >> _______________________________________________ >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >

1 0

ChimeraX question - Diana Mayorga
by Diana Carolina Mayorga Gonzalez 27 Jan '25

27 Jan '25

Hi, Hope you are well. I would like to know if I can do these transparent bubbles in ChimeraX showing the atoms stick as well. If it is possible, could you help me with a small tutorial, please? [cid:add7b0b3-f091-48a9-bc44-329473b06f2e] Thank you so much in advance, Diana Carolina Mayorga G PhD Student Yannick Doyon Lab Research Center - Université Laval Department of Reproduction, mother and youth health (RSME) Québec, Canada

2 1

Re: movie with model label/name
by Elaine Meng 26 Jan '25

26 Jan '25

Dear Saif, To ask questions in the future, we recommand that you please use the mailing list for the appropriate program (chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> for Chimera, chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> for ChimeraX). If you mail me individually your question may not get answered. I will answer for ChimeraX since that is our preferred program now -- Chimera is no longer developed. In general, this topic is covered in the ChimeraX "making movies" page: <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html> You can do all of this with a command script using several commands. There is a "morph" (atomic) or "morph maps" (density maps) command to do the morphing. You would probably change the display (colors, styles, etc.) to how you want it for your movie and then save a session. Then, to work on making a movie you would create a command script that applies to the session. The reason to save a session is so you can avoid redoing the same setup calculations, coloring, etc. every time you run the script. You can do all that stuff first and then save a session. Usually working on the script takes several days, so you would just restore your session and then continue working on the script. The script would contain what you actually want to show in the movie. You can play back an atomic morph with "coordset" and show/hide labels with "2dlabel" and you can do all kinds of other stuff as well, like zoom and rotate. You may also want to save positions in your session file (see "view" command) and then during the movie script, restore those different positions. When the movie script contains what you want to show in your movie, which is usually a long interative process after you play it back several times and keep changing the commands, then you would add the movie-recording commands (see "movie" command) to start recording at the beginning and save the movie file at the end. There are examples in our "making movies" page and links therein to the help for the commands mentioned above as well as movie-making tutorials. 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 Jan 26, 2025, at 5:53 AM, Md Saiful Islam - MRC LMB <sislam(a)mrc-lmb.cam.ac.uk> wrote: > > Dear Elaine > Just wondering, is there any script to make movies to show the conformational changes between multiple models with the labeling of each of the models shown. > For example, I want to make a movie to show a morph between three cryoEM models where I want to label the three models while morphing from model 1 to model 2 and from model 2 to model 3. > > Accept my apologies if you already shared this before. > > Many thanks for your help. > > Kind Regards > Saif

1 0

Confirming coordinate axis
by Abhinaba Das 24 Jan '25

24 Jan '25

Dear ChimeraX-users, I'm writing to ask if there is a way to view the x,y,and z axis live while model building. I've a helical map generated in CryoSPARC which has a D1 symmetry. I could generate the asymmetric unit (ASU) for the corresponding C1 reconstruction but having issues applying D1 symmetry. The approach I've taken is to make a diheral copy of the C1 ASU (turn y 180 center <mapId> coordinateSystem <mapId> model <modelid>; followed by combine command). This should generate the dihedral ASU, and if the helical symmetry is applied should generate the symmetric copies (?). But seems not to be working.. I've assumed that the dyad axis is along the y-axis (cryosparc says for its output map). Just wondering if the axes are aligned.. Thanks, Abhi

3 2

openmmforcefields
by Lewandowski, Jozef 24 Jan '25

24 Jan '25

Hi, I really like that openmm is implemented in ChimeraX. Is it possible somehow to implement/include openmmforcefields (https://github.com/openmm/openmmforcefields)? Specifically, I often use custom residues and would love to, e.g. parametrise them using GAFF, to do some small local minimisation in ChimeraX. Or is there any way of passing force fields for ligands parametrised with GAFF to ChimeraX? Thanks, Józef

3 2

Surface Color
by Hansen, Bryan (NIH/NIAID) [E] 24 Jan '25

24 Jan '25

Hi, I'm having issues with coloring a surface by volume. When I compare the two volumes I don't get the larger volume completely colored and even when I set 'Color outside volume' to match the same color as the 0 value which in this case is the blue it still renders grey. Can you help me with which step I'm messing up? Thanks. Bryan Hansen Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU Rocky Mountain Laboratories 903 S. 4th St Hamilton, MT 59840 406.363.9202 *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************

2 3

Assigning a custom net charge for a ligand using dockprep
by Jade Shi 24 Jan '25

24 Jan '25

Hi, I am trying to use dockprep to prepare PDB files with ligand molecules for subsequent modeling and analysis. I am currently using the "dockprep" command with no additional arguments. However, I find that occasionally when calculating partial charges using antechamber/AM1-BCC, ChimeraX assigns an incorrect total charge to the ligand resulting in an incorrect charge distribution. Is there a way to specify this manually, i.e. the equivalent of supplying the -nc flag when using antechamber directly? Thanks a lot! Jade

2 1

Draw and build secondary structures interactively
by Roden Deng Luo 22 Jan '25

22 Jan '25

Hi, I know there is a tool and command "build". But it is not that interactive. I wonder if there is a feature in ChimeraX (or any other tools) that can allow the user to draw in 3D space (or 2D) lines and then specify some segments as alpha-helices and some other segments as beta-sheets. I imagine the generated structure can be a backbone populated with G (glycine). Thanks, 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.

2 2

"forEach" command to open multiple pdb from multiple directories and save images there ?
by Vincent CHAPTAL 21 Jan '25

21 Jan '25

Hi, I would like to open multiple alphafold results that are stored in several folders, make an image, and save the image in those orignial folders. I'm using the forEach command to open all the results and run the script to create an image, and it works very well: open script.cxc forEach /PATH*/ranked_*.pdb script.cxc: open reference-structure.pdb match #1 to #2 color #*/B green color #*/C red color #*/D blue view matrix camera 0.87509,0.019021,-0.48356,-124.35,0.48393,-0.035333,0.87439,694.49,-0.00044561,-0.99919,-0.040123,163.41 I'm only stuck at the saving process where I'd like to save an image ranked_*.png matching the original name and folder location: save /PATH*/$file.png doesn't work because the /PATH*/ is not recognized as an existing directory. save /$PATH*/$file.png gives the same error. If I remove the /PATH/ it saves all the images on top of each other and it defeats the purpose. Could you let me know how to save in the folder where the .pdb was read from? 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

UCSF ChimeraX - Using the software for teaching
by Fernandes, Clive 17 Jan '25

17 Jan '25

Dear Team, Hope the new year is treating you well. I'm Clive Fernandes, working within the Technology Procurement Team at Imperial College London. A member of the teaching staff has contacted me to inquire whether they can use ChimeraX for teaching purposes. This would involve installing the software in a few small lab/teaching rooms. Could you please confirm if this use is permissible and does not violate the terms and conditions? Thank you. Best wishes, Clive Fernandes Software Asset Management Lead Information & Communication Technologies Level 4, Sherfield Building Imperial College London South Kensington London, SW7 2AZ Connect on LinkedIn<https://www.linkedin.com/in/clive-fernandes-/>

2 2

Regarding the issue of residue display
by 张馨丹四川大学生物治疗国家重点实验室 16 Jan '25

16 Jan '25

There are gaps between adjacent residues sticks and cartoons. How should this problem be solved? Looking forward to your reply. Thank you!

2 2

No command line or the right-side tap in ChimeraX1.9
by Chloe Chin 16 Jan '25

16 Jan '25

Hi, I'm an undergraduate student who just started to use ChimeraX! Unfortunately, I found that ChimeraX1.9 did not show any command line or the tap that should be shown in the right-side (where we can see the log). However, it appears when I use ChimeraX 1.10. Can anyone let me know what might be wrong? Also, will there be any problem if I just use ChimeraX 1.10 (or the daily build, because I downloaded the daily exe and it became 1.10)? My laptop is window 11 by the way. I'd appreciate it a lot if I could get an answer for my questions... I'll be waiting for the reply :) Best, Chloe

2 1

Different dihedral angle results between Chimera and ChimeraX
by Alexander Hung Lee 16 Jan '25

16 Jan '25

Hello, I was looking to calculate the dihedral angle, and ChimeraX was giving me a value that I didn't agree with. I ran the same command with the older Chimera, and it's more in line with what I expected I was looking at the dihedral angle for N-acetyl in sialic acid. ChimeraX gave me 6.9 degrees while Chimera gave me -179.95 degrees. Is there something wrong that I'm doing? It's from the same pdb file. [cid:d7d74402-46c4-4f1e-8ee1-2d78698cb88f] Regards, Alex

2 2

Question about the tool Find Cavities
by svle＠tiscali.it 16 Jan '25

16 Jan '25

Hi, the tool Find Cavities returns as information about each detected cavity the number of points describing the what has been found. It is possible to obtain the coordinate of that points so to calculate the "center" of a found cavity of interest? Thanks. Saverio

3 4

pb with alphafold error plot when we used dimer
by Jean-François Bureau 15 Jan '25

15 Jan '25

Hi, When I stimulate dimer using alphafold3, it is not possible to load the error plot since Chimerax is waiting to have the data of the first protein and find that of both. Best JF Bureau

2 1

Re: From the Correct email now: ChimeraX corrections for the getting started tutorial.
by Elaine Meng 13 Jan '25

13 Jan '25

Hi Anne-Francis, For ChimeraX, we don't have an exact parallel to the "getting started" tutorial for Chimera. However, the one I usually recommend as an intro to general molecular modeling (such as for a class) is Protein-Ligand Binding sites <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> You can also look down through the tutorials index to see if there are any more specific ones that might interest you. <https://www.rbvi.ucsf.edu/chimerax/tutorials.html> The ChimeraX "quick start" sections can be followed sequentially as they are written, but I understand it is not really the same kind of narrative as most tutorials. You may also be interested to try the "click to execute" approach where you don't even have to type the commands (although perhaps it does not provide as much reinforcement for the students to learn them). Regards, 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 Jan 12, 2025, at 7:01 PM, Anne-Frances Miller <afmill3r2(a)gmail.com> wrote: > > Oh shoot! > You are right, > > I see how that happened though, for the ChimeraX https://www.rbvi.ucsf.edu/chimerax/tutorials.html > I don't see any getting started guide that leads people though all the basics from start to finish with commands being introduced. > > Have you got such a thing yet? This class cannot use the quick start guide, they need a full work flow. > > This one gets close: https://dasher.wustl.edu/bio5357/software/chimerax/tutorial.pdf > > THANK YOU for answering on a Sunday!! > Anne-Frances > >

3 3

abbreviation for transparentbackground please
by Anne-Frances Miller 12 Jan '25

12 Jan '25

Dear Sir or Madam, Re. ChimeraX 1.7: the image save option ’transparent background true’ is very long, and typo-prone. Is there an abbreviation or short form please? Thank you - • - • - • - • - • - • - • - • - A.-F. Miller, Ph. D. (she/elle/sie) University Research Professor Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin

5 8

Problem upgrading to the latest version 1.9
by svle＠tiscali.it 09 Jan '25

09 Jan '25

Hi, surely for my errors in uninstalling the previous version , I'm receiving the following: $ sudo apt remove --purge ucsf-chimerax Reading package lists... Done Building dependency tree... Done Reading state information... Done The following packages were automatically installed and are no longer required: libgdk-pixbuf-xlib-2.0-0 libgdk-pixbuf2.0-0 libosmesa6 libxcb-cursor0 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: ucsf-chimerax* 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 0 B of additional disk space will be used. Do you want to continue? [Y/n] (Reading database ... 524167 files and directories currently installed.) Removing ucsf-chimerax (1.9ubuntu24.04) ... Deregister desktop menu and associated mime types /var/lib/dpkg/info/ucsf-chimerax.prerm: 4: chimerax: not found dpkg: error processing package ucsf-chimerax (--remove): installed ucsf-chimerax package pre-removal script subprocess returned error exit status 127 dpkg: too many errors, stopping Errors were encountered while processing: ucsf-chimerax Processing was halted because there were too many errors. E: Sub-process /usr/bin/dpkg returned an error code (1) $ dpkg --get-selections | grep ucsf ucsf-chimerax install $ chimerax chimerax: command not found Any suggestions to recover? Thanks. Saverio

2 1

Volume eraser as cube?
by Oliver Clarke 09 Jan '25

09 Jan '25

Hi all, Hope the chimeraX team & community are having a great start to 2025! There are often situations (in single particle cryo-EM) where I would like to erase using a plane rather than a sphere - e.g., when I want to chop off density protruding from a nanodisc or micelle in order to make a mask. There are various workaround ways to do this (e.g. just making the sphere enormous, making a cubic/rectangular mask and multiplying/substracting, etc), but I was wondering if this is a common enough scenario (perhaps other users can chime in?) that it might be worth adding the option of erasing using a cube rather than a sphere? Cheers Oli

2 1

Saving restraints
by Dyda, Frederick (NIH/NIDDK) [E] 07 Jan '25

07 Jan '25

I was wondering if there is a way to save restraints that one set up for a particular structure. For instance if I set up a bunch of "Simple Distance Restraints" in Isolde, to restrain a metal coordination environment, can I save these so I can reuse them for another .pdb file (assuming residue numbering is the same). Thanks. Happy New Year! Fred ******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 NIDDK Bldg. 5. Room 338 e-mail: Fred.Dyda(a)nih.gov Bethesda, MD 20892-0560 URGENT message: 2022476710(a)msg.fi.google.com Google map: 39.001168, -77.102048 http://www-mslmb.niddk.nih.gov/dyda/dydalab.html *******************************************************************************

2 2

Assistance/guidance with ChimeraX
by Mahesh Chandrasekharan 03 Jan '25

03 Jan '25

Hi: First up, thank you and your team for all your efforts in creating and maintaining Chimera and ChimeraX. They are an awesome tool/package! It would be very helpful if you could please assist me with the two questions below. 1) I have a PDB downloaded from Alphafold. I would like to ‘drag out’ or reposition regions in order to enable their better visualization for a figure that I need for a grant. How can I select and reposition specific regions of a protein structure in ChimeraX? 2) The protein of my interest is a homodimer. I would like to open two copies of the relevant PDB file and manipulate them as two separate proteins. I have made a duplicate and relabeled the PDB file. However, when I open it ChimeraX along with the original, the two files seem linked, and I am unable to work on them separately. Is there a way to open two copies of the same PDB file to ‘recreate’ a homodimer? Thank you, Best, Mahesh Mahesh B. Chandrasekharan, PhD Assistant Professor of Radiation Oncology Investigator, Huntsman Cancer Institute Adjunct Assistant Professor of Hematology & Hematological Malignancies University of Utah School of Medicine 2000 Circle of Hope Room 3715 Huntsman Cancer Institute Salt Lake City, UT 84112-5540 Phone: 801-213-4220 Administrative Assistant: Coreen Rankin (801-585-3599) Lab site: https://uofuhealth.utah.edu/huntsman/labs/chandrasekharan

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Getting average of PAE values for a given region / interaction
by David S. Fay 02 Jan '25

02 Jan '25

Greetings and Happy New Year to All! My question is about broadly protein-protein interactions (PPIs. Last year several manuscripts came out proposing new metrics for assessing PPIs. This was in logical response to the growing understanding that ipTM (alone) is a fairly flawed metric, particularly for detecting interactions that involve a small number/fraction of the total residues. For those interested, I’ve pasted links to three such papers below (Coincidentally one is from a former roommate's lab, which I didn’t notice until recently!). Some may be easier to use than others (have GUIs). Tom Goddard and I emailed back and forth a bit about the relative merits of some of these metrics - nothing is perfect obviously (thank you again Tom). With respect to ChimeraX, I was wondering if there was a way to extract average PAE values after employing a cutoff. For example, "alphafold contacts /A distance 5 maxPae 5” will tell me that are "54 residue or atom pairs within distance 5 with pae <= 5”. But what if I want to know the average of those 54? Along those lines, for some PPIs there may be several spatially separated interfaces, with each one contributing to the total number. Is there an easy way to obtain the average and other metrics for each one? Some of this information I could probably find in my clunky (borderline boomer) way, by filtering, adding, and averaging values from the pairwise data (perhaps made easier by Predictome). Lastly, drawing rectangles on the PAE plot does a great job of giving coordinates and the average PAE, but it doesn’t give the range or other potentially useful data, such as the number of PAE<5 values etc. I guess I’m thinking that it could be very useful to be able to get metrics for a prescribed region of the PAE plot simply by drawing the rectangle. (And maybe there is but I missed it.) Those are my questions and thoughts. But I also wanted to express my gratitude for the ChimeraX software, and even more, the people working at ChimeraX who are always exceptionally responsive and helpful. David https://www.biorxiv.org/content/10.1101/2024.02.19.580970v1 https://www.biorxiv.org/content/10.1101/2024.10.23.619601v1 https://www.biorxiv.org/content/10.1101/2024.04.09.588596v1 David S. Fay Ph.D. Professor, Department of Molecular Biology Associate Director, National Institutes of Health Wyoming INBRE University of Wyoming email: davidfay(a)uwyo.edu

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get help with changing the cartoons ribbon to ball sticks
by Nhi Hoang 02 Jan '25

02 Jan '25

Hi. I am a sophomore at Le Quy Don High School in Danang City, Vietnam. I am using ChimeraX to display a model for my little project, and I have found a small trigger that I want to get help with. My problem is I cannot change the cartoon of selected residues from ribbons to ball sticks, after I have preset the model with cartoon ribbons. I wonder if this problem is due to the application and its limits or because of my device. I have attached an image presenting the coding and the model for a clear description of my problem. If possible, I am really willing to receive some advice from you in tackling this problem. Thank you very much. Best, Nhi Hoang. [image: image.png]

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Vector in ChimeraX
by Vitali James 30 Dec '24

30 Dec '24

Dear ChimeraX, Can you please help me to connect two pseudo-atoms by vector in ChimeraX. In the attached image (chimera.png), it was smoothly done in the past, but now the same file looks like a dotted line in chimeraX( e.g vector.PNG). Is it possible to control the color and style of this dotted vector line? best regards J. Vitali

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Quest 2 Support?
by Blaine Hewitt 27 Dec '24

27 Dec '24

Hello, my name is Blaine Hewitt. Now I know that you have stated previously that you have no intention of bringing support to the Oculus Quest. Which is completely understandable since I know that not only would you have to develop around a completely new Operating System but another CPU architecture and much much more I assume. But with the soon release of the Oculus Quest 2 and it's new XR 2 chip-set makes a pretty good argument for it. As this would allow for much easier use in education (as is what I am attempting to do with it). I think it will be even easier now to push updates with SideQuest <https://sidequestvr.com/> being relatively simple to setup. I know that another (Naome <https://blog.matryx.ai/nanome-on-quest-public-beta-is-now-available-b546321…>) program is already available on the platform. But I do like your program a lot more since it is able to be used for free unlike Nanome Pricing <https://nanome.ai/pricing/> which is... as to say unappealing to public schools (such as mine). I was was also thinking (sorry if I am becoming annoying at this point) that if you do make a version of the Quest that you could make that GitHub branch available to the public. As for example while I may not be great at understanding complex protein structures I can help to make the whole experience more user friendly. Anyways if you read this far thank you for taking time from your day to read this. If you want to know who I am, my name is Blaine I am in my senior year of High School (Waynecsd <https://wh.waynecsd.org/>). I have to do a project by the end of the year where I have to present an area of study I want to pursue and I decided to research the effects of VR on the human's ability to learn and retain information. Budget..... None

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Unable to show interactions between bases and protein
by ADINDA 27 Dec '24

27 Dec '24

Dear Chimerax team, Hi, I am trying to find the interactions between my RNA and protein but have been unable to do so. I've been using the "contacts" function but it's not been working as expected. The command line that I gave was: contacts #1.2 restrict #1.1 makePseudobonds true reveal true log true where #1.2 is my RNA and #1.1 is my protein. Even when I switch the positions of #1.2 and #1.1, it still doesn't work (0 contacts shown). Do you have any tips on how I can rectify this? Happy holidays! Best regards, Adinda

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