- ChimeraX-users - RBVI Mailing Lists

Edit right mouse labels?
by Oliver Clarke 10 Jun '25

10 Jun '25

Hi, There is probably an easy way to do this but I could not find it in the GUI. Is there a way to edit labels placed with the right mouse? Currently they only give the residue type and number, there doesn't seem to be a way to edit or configure them in the same way as one can do using the global per-residue labels in Actions>Labels. If it doesn't exist, perhaps a right mouse mode "Edit label" would be useful to complement Label and Move Label? This would be helpful when making a quick movie to show density quality, and would allow one to easily add custom labels without needing to use the CLI. Cheers Oli

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Boltz-2
by Lynne Howell 10 Jun '25

10 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

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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

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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

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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/

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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/ >>

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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

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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/

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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

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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

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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

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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

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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/

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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.

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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

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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.

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