- ChimeraX-users - RBVI Mailing Lists

Building ions using ISOLDE
by Przemyslaw Dutka 22 Oct '25

22 Oct '25

Hello, I am currently encountering an issue while trying to build Na ions with ISOLDE. Despite various attempts, the ions consistently move outside the density as soon as the simulation begins. The ion site is clearly defined by previous crystallography maps. I have also downloaded several EM maps that include modeled Na ions, such as PDB 6VWX (see below). In these cases, the ion still moves up or down the channel once the simulation starts. The only method I've found to keep the ion in place is by pinning it. I would greatly appreciate any advice or tips. [image: Screenshot 2025-10-21 at 10.33.05 PM.png] Best, Przemek

2 1

building on macOS
by Alexis Rohou 21 Oct '25

21 Oct '25

Hello, I'd like to build from source in order to play with (and possibly hack at) the MCP server. I am on macOS 14.7.6 with Xcode 16.2. I think the compilation went well, but at link time I get warnings and an error. Below is the end of the output of `make install`. What do you recommend I try? Cheers, Alexis available bundle cache has not been initialized yet Executing: devel install . user false exit true noDeps true ld: warning: object file (/Users/rohoua/work/git/ChimeraX/src/bundles/atomic_lib/atomic_cpp/pyinstance_cpp/PythonInstance.o) was built for newer 'macOS' version (11.0) than being linked (10.9) ld: warning: object file (/Users/rohoua/work/git/ChimeraX/src/bundles/atomic_lib/atomic_cpp/element_cpp/Element.o) was built for newer 'macOS' version (11.0) than being linked (10.9) ar: src/lib/libatomstruct_tmpl.a is a fat file (use libtool(1) or lipo(1) and ar(1) on it) ar: src/lib/libatomstruct_tmpl.a: Inappropriate file type or format Traceback (most recent call last): File "/Users/rohoua/work/git/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/_distutils/spawn.py", line 87, in spawn subprocess.check_call(cmd, env=_inject_macos_ver(env)) File "/Users/rohoua/work/git/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py", line 413, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/usr/bin/xcrun', 'ar', 'rcs', 'src/lib/libatomstruct_tmpl.a', 'atomic_cpp/atomstruct_cpp/tmpl/Atom.o', 'atomic_cpp/atomstruct_cpp/tmpl/Bond.o', 'atomic_cpp/atomstruct_cpp/tmpl/CoordSet.o', 'atomic_cpp/atomstruct_cpp/tmpl/Molecule.o', 'atomic_cpp/atomstruct_cpp/tmpl/Residue.o', 'atomic_cpp/atomstruct_cpp/tmpl/TemplateCache.o', 'atomic_cpp/atomstruct_cpp/tmpl/amino.o', 'atomic_cpp/atomstruct_cpp/tmpl/camino.o', 'atomic_cpp/atomstruct_cpp/tmpl/findres.o', 'atomic_cpp/atomstruct_cpp/tmpl/general.o', 'atomic_cpp/atomstruct_cpp/tmpl/ions.o', 'atomic_cpp/atomstruct_cpp/tmpl/namino.o', 'atomic_cpp/atomstruct_cpp/tmpl/nucleic.o']' returned non-zero exit status 1.

2 3

questions for ChimeraX
by Jéromine Carret 21 Oct '25

21 Oct '25

Hello, My name is Jéromine, and I am a PhD student at the University of Lille, France. We are working on structural modelling of different protein variants. We have questions about the ChimeraX software tools. We would like to obtain electrostatic maps of protein structures and avoid using the colour scale in order to obtain numerical results. And also for hydrophobicity maps. We also want to study the clashes between the positions of variants. Do you have any advice? For the matchmaker command, can you give me the information I need to understand the results? Thank you in advance for your reply. Kind regards. Jéromine Carret PhD candidate RADEME lab ULR 7364 Université de Lille

2 3

chimeraX daily built, 2025 Oct 20, boltz-2 empty sequence line in yaml file
by Guenter Fritz 20 Oct '25

20 Oct '25

Dear ChimeraX developers, really a great job implementing boltz into chimeraX !! I have just installed the latest daily build 2025 Oct 20 on a Redhat 8 (Rocky 8 derivative) machine. Boltz-2 installs with no visible problem via chimeraX (like before). When I try to run predictions, I get an error which seems to be due to an almost empty yaml file created by chimeraX. Only the first line ("version 1.0") is in the yaml file. Boltz (of course) fails. There should be no problem with permissions. I just installed also the latest release of chimeraX and boltz-1 via chimeraX. Runs as expected. PS: I had no try yet on my mac (will check later). Best wishes, Guenter

2 3

Problems adjusting the phi/psi angles with ChimeraX
by Gong, Zhen 15 Oct '25

15 Oct '25

Dear ChimeraX team, I was trying to use ChimeraX to change the phi/psi angles of a residue in the loop region but encoured this error: ILE 411 N ↔ CA is part of a ring/cycle and cannot be rotated. There is no ring/cycle in ILE411 or neibouring residues: ASN 410 or THR 412. I tried ChimeraX daily (version 1.10.dev202504260127 (2025-04-26) and ChimeraX 1.10.1 but the same error happened. I am wondering if it is possible to change the phi/psi angles with ChimeraX. Thank you. Best, Zhen

2 3

Chimera and ChimerX issues after update to MacOS Tahoe
by Rechiche, Othman 14 Oct '25

14 Oct '25

Hi everyone, I recently updated to MacOS Tahoe, Since then I encountered several issues with Chimera, ChmieraX and python. I installed and removed and reinstalled the apps but I still get the same error. For chimera I get this error: [Screenshot 2025-09-24 at 12.08.51 AM.png] FOr ChimeraX, when I try to open a session, it complains that the session was created with another version of python. I opened that session successfully several times before to the update of MacOS and I have never seen this error before. Failed opening file /Users/x/x/x/x/x/x/x/x.pyc: Python code was compiled for a different version of Python Can you please help me fix this? Best Regards, Othman Dr. Othman Rechiche Herbert Irving Comprehensive Cancer Center Columbia University Medical Center Columbia University New York, NY 10032 email: or2296(a)cumc.columbia.edu phone: +1 (814) 880-5554

3 4

help on color command
by James Raymond 12 Oct '25

12 Oct '25

Dear ChimeraX, I have tried 100 variations of color command without success. Can you tell me the command to color residues 132-145 red in this single chain protein? thank you Jim [image: image.png]

2 1

Issue with combining two pdb models in chimeraX
by Rayees Mattoo 10 Oct '25

10 Oct '25

Hi, I have two models #1 Model1.pdb and #2 Model2.pdb having one shared polypeptide, same chain ID but different residue numbers. I wanted to combine them to make a merged_model #3. I used the following combine commandline in chimeraX: combine #1 #2 close false modelId #3 retainIds true name merged_model The resulting combined model appeared to be correct, and I proceeded to run phenix.real_space_refine without any issues. However, when I attempted to deposit the refined model (either in .pdb or .cif format) with the wwPDB, I received a file with multiple errors (see attached). Interestingly, I had previously deposited the individual models (#1 and #2) without any problems. This situation raises my concern about whether the combination process was successful. Is there anything I should have done differently to ensure a seamless combination of the models? Best Rayees

2 1

ChimeraX-1.10.1 syntax issue
by wwvivian.wang＠mail.utoronto.ca 10 Oct '25

10 Oct '25

Hi, this is my first time using ChimeraX-1.10.1 and I ran into a little bit of trouble with syntax errors in this version.\ I opened a pdb file that contains two chains of proteins that I'm interested in - Chain A and B. I then renamed and coloured them to Chain C and D for clarity. In the Contacts window, I made the following changes: Find pairs of atoms with: ✅ VDW overlap ≥ –0.4 Å Limit by selection: ✅ with at least one end selected Ignore interactions between atoms 4 or fewer bonds apart: ✅ Ignore interactions between residues <5 apart: ✅ Include intermodel: ✅ Include intramodel: ❌ (uncheck it) Include intramolecule: ❌ (uncheck it) Ignore hidden models: ✅ Display as pseudobonds: ✅ (keep green, radius 0.075, dashes 6) Write info to: Log ✅ Then click Apply I then selected the atomic model #1 (Chain C+D) and deselected surface models #1.1 (Chain C) and #1.2 (Chain D) and ran the Contacts Command: "contacts atoms #1/C #1/D makePseudobonds true distanceCutoff 4.0 log true" but the software returns "Expected a keyword" argument and highlighted "distanceCutoff 4.0 log true" in red. Alternatively, I also tried "findclash #1/C test #1/D overlapCutoff -0.4 hbondAllowance 0 interModel true intraMol false intraRes false makePseudobonds true select true log true" but again it fails to output contact coordinates between the two chains and returns the following: "Unknown command: findclash #1/C test #1/D overlapCutoff -0.4 hbondAllowance 0 interModel true intraMol false intraRes false makePseudobonds true select true log true". I would appreciate your help in resolving this error for me. Thanks, Vivian

2 1

Focus in ChimeraX
by Luca Pellegrini 10 Oct '25

10 Oct '25

Hi, What is the ChimeraX equivalent to the Focus command in Chimera? I have selected a portion of a structure, and would like to bring it into focus without dragging it into view. Also Focus would automatically set the selection as the pivot point. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA lp212(a)cam.ac.uk

4 3

Question about using ChimeraX
by 张圃源 09 Oct '25

09 Oct '25

Hi， I'm a new user of ChimeraX and I'm currently facing a problem. I want to convert a pdb file into an mrc file that can be input into cryoSPARC, and this mrc file should be in the form of a cube volume. I will use ChimeraX to achieve this. How should I proceed? Best Yuan 中山大学张圃源

2 1

tools for ligand-receptor interactions
by Elaine Meng 09 Oct '25

09 Oct '25

> On Oct 8, 2025, at 9:58 AM, Vojo P Deretic <VDeretic(a)salud.unm.edu> wrote: > > Hi > How do I pose a question - via email or on the site? > My question is: we have a Boltz/alphafold fitted organic molecule into a known structure. > What are the tools for residue interactions in ChimeraX apart from H bonding and hydrophobic or charged surfaces? > Thanks > Vojo Deretic > Hi Vojo, As per the Contact Us page <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html> ...to ask questions you would use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address, which is CC'd here so you don't need to send your questions again. I don't know what you mean by "on the site" since there is no webform for questions, only this email address. You already mentioned H-Bonds and coloring the receptor molecular surface by ESP (electrostatics) or MLP (lipophilicity). That's most of it. Certainly you can just visually evaluate what is nearby, but you could use the Contacts tool for a more objective approach: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> See also the tutorial "Protein-Ligand Binding Sites" <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.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 Oct 8, 2025, at 9:58 AM, Vojo P Deretic <VDeretic(a)salud.unm.edu> wrote: > > Hi > How do I pose a question - via email or on the site? > My question is: we have a Boltz/alphafold fitted organic molecule into a known structure. > What are the tools for residue interactions in ChimeraX apart from H bonding and hydrophobic or charged surfaces? > Thanks > Vojo Deretic > > Sent from my iPhone with lots of typos and autocorrect nonsense - my apologies... >

2 5

Append ligand coordinates from one PDB to another
by George Tzotzos 08 Oct '25

08 Oct '25

I’m dealing with two structurally similar proteins, one of which is in complex with a ligand (pdb1). The second protein is in the apo-form (pdb2). I’ve used matchmaker to superimpose the structures. Does it make sense to append the ligand coordinates to pdb2? I’m interested to find out which residues lie within 4-5 Å from the ligand. Probably a better approach would be to dock the ligand to pdb2. Could this be done through ChimeraX using Boltz2? Thank you for your suggestions. George

2 2

Issue in displaying pdb in chimeraX
by Rayees Mattoo 07 Oct '25

07 Oct '25

Hi, I merged two molecules in coot and generated a merged.pdb file. However, upon displaying in ChimeraX part of my model is cartoon and part of it displays as worm, see the attachment. After running dssp I can fix it, but I want it to display as cartoon by default. Anything I need to edit in the merged.pdb file? Best Rayees

2 1

Modeller interface
by Alexandra Zahradnikova 07 Oct '25

07 Oct '25

Hi All, Today I am getting problems when trying to model loops with Modeller. Repeatedly (on different structures), the following error occurs: modeller refine 1/A:1:internal-missing numModels 1 fast false adjacentFlexible 1 protocol standardException in thread Thread-33 (_run_function): Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.10\bin\Lib\threading.py", line 1038, in _bootstrap_inner self.run() File "C:\Program Files\ChimeraX 1.10\bin\Lib\threading.py", line 975, in run self._target(*self._args, **self._kwargs) File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-packages\chimerax\core\tasks.py", line 300, in _run_function func(*args, **kw) File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-packages\chimerax\webservices\cxservices_job.py", line 156, in run reason = json.loads(e.body)["description"] ^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10\bin\Lib\json\__init__.py", line 346, in loads return _default_decoder.decode(s) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10\bin\Lib\json\decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10\bin\Lib\json\decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0). Is it a problem with the Modeler server? How can I find out in the future whether there is a problem with the server or the problem is in my input structure? Thanks in advance. Best regards Sasha

2 2

Re: [Chimera] local resolution map colors
by Elaine Meng 06 Oct '25

06 Oct '25

I can't tell anything from the image, since I have no idea what your filenames mean. All I can say (again) is you have to open both the original map and the local resolution map, show the original map as a surface, and use the local resolution map values to color that surface. Elaine > On Oct 3, 2025, at 2:32 PM, Roy Chowdhury, Shatabdi <Shatabdi.RoyChowdhury(a)ucsf.edu> wrote: > > Hi Elaine, > > Thanks for your reply. Attaching the new screenshot here. This shows that the map values are 0.1095 all over. Please let me know if I can give any additional information. > ~Shatabdi > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Friday, October 3, 2025 2:20 PM > To: Roy Chowdhury, Shatabdi <Shatabdi.RoyChowdhury(a)ucsf.edu> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera] local resolution map colors > !-------------------------------------------------------------------| > This Message Is From an External Sender > This message came from outside your organization. > |-------------------------------------------------------------------! > > Hi, > This question was sent to the commercial licensing address -- for user questions, please use the email address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here to ensure that you get an answer instead of mystified silence. > > Is the local resolution map open in addition to the original map? I only see two copies of the same map in the Volume Viewer. Make sure that you open the local resolution map instead of a second copy of the original map. > > 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 Oct 3, 2025, at 2:07 PM, Roy Chowdhury, Shatabdi wrote: > > Hi, > > > > In the past, I've used chimerax to display local resolution on maps using the tools->volume data->surface color function. In a new map, I'm having difficulty with it. I'm attaching screenshots where the phenix local resolution job suggests the resolution range to be 1.27A - 4.6A range which is in agreement with cryosparc. When I load the cctbx_program.ccp4 file on chimerax, it is unable to color the surface and says the surface values are -0.067 - 0.107. Is there something I should be doing differently? Any suggestions would be deeply appreciated. > > > > Thanks! > > > > Shatabdi Roy-Chowdhury, PhD. > > Cardiovascular Research Institute > > University of California, San Francisco > > > <Screenshot from 2025-10-03 13-56-32.png><Screenshot from 2025-10-03 13-56-51.png>> _______________________________________________ > > Chimera mailing list -- chimera(a)cgl.ucsf.edu > > To unsubscribe send an email to chimera-leave(a)cgl.ucsf.edu > > > <Screenshot from 2025-10-03 14-29-30.png>

2 4

Issue with the coordset slider in chimeraX
by jeandidier.marechal＠uab.cat 05 Oct '25

05 Oct '25

Hi everyone, I am starting to take steps into ChimeraX handlers of MD simulations. So far, there have been no problems loading the starting PDB file and the trajectory. However, I am unable to make the coordset slider work. I always have the minimal version with the frame slider, the snail, and the recording button. Nothing happens when running the coordset slide #number_of_the_model. So, I can not make distance plotting and so on. I tried different versions of the software, including the latest daily build and the most recent production release. Thanks a lot for telling me what I do wrong and, if not readily implemented, please apologize for my impatience ;-) Cheers JD

2 1

Struggling to complete assignment at last minute? Hire our Assignment helper
by mglen142＠gmail.com 04 Oct '25

04 Oct '25

Being a student, you may juggle several things in academics. Students are burdened with several academic tasks. Managing lectures, self-study, homework, exams, tests, and academic projects at the same time can be difficult for students. Sometimes students forget the deadline and seek urgent help for the academic assignment. Seeking last-minute writing assistance, you can connect with our <b><a href="https://us.assignmenthelppro.com">Assignment Helper</a></b> in the USA. They can help you to complete the assignment timely and excellently. The experts are trained to work fast on academic assignments. Professional experts are ready to assist students at any time with any type of writing need. With their support, you can complete the assignment on time and meet the urgent deadline. Their support allows students to manage busy schedules and focus on learning other necessary things or mastering the subject.

1 0

Save centroids in scene coordinates
by Andrew Kennard 03 Oct '25

03 Oct '25

Hi there, I have aligned a bunch of models with matchmaker, and then I defined centroids for each model with `define centroid`. I would like to export those centroids for further analysis (trying to see the spatial relationship between chains B from each model when all models are aligned on chain A). However, the only way I could figure out how to do it was to press "Save Info..." in the Structure Measurements window. This text file reports the centroids in the model coordinate system for each model. But because I aligned the models with matchmaker, I'd rather have the centroids in the scene coordinate system. I am not sure how to do this transformation and export all the coordinates (~dozens of models). The only other option I found that might work was the `getcrg` command which I could use to save the coordinates to the Log, but then I will have to save the log as an HTML and parse that, right? Is there any more straightforward way? Alternatively, is there a better way to define centroids (ideally programmatically) so I can extract them from Chimera easily in scene coordinates? Perhaps the measure center command is the thing I should be using? Thanks a bunch! I'm running ChimeraX v1.10.1 (2025-07-24) on Mac OS 15.6 Sequoia Thank you!! Andrew

2 3

de novo octahedral assembly of AlphaFold-generated ferritin monomers
by jmcquaid＠ucsd.edu 03 Oct '25

03 Oct '25

Hi folks! I would like to use "Sym # O" to model how a novel marine ferritin might assemble into an octahedral nanocage. Like ferritin, this marine ferritin is thermostable and has a size consistent with a 24-mer, but the AA sequence is too divergent to use 'matchmaker'. I've noticed that if I create a fold model of human ferritin (1FHA) with AlphaFold and import it into ChimeraX, the 'sym # O' command generates a 24-mer hairball rather than an octahedrally-coordinated sphere. If I 'fetch' the same 1FHA protein directly from PDB, the spherical structure is correctly assembled. What additional commands might be needed to help ChimeraX correctly assemble an AlphaFold-generated 1FHA monomer into the canonical ferritin cage? Chimera used to have a 'group 432' command, but I see this is not currently supported. Thanks in advance! Knowing how to correctly assemble something known like human ferritin will greatly help in assembling something unknown like a marine ferritin. Best Regards, Jeff McQuaid, Scripps Institution of Oceanography

3 4

Re: [Chimera] local resolution map colors
by Elaine Meng 03 Oct '25

03 Oct '25

Hi, This question was sent to the commercial licensing address -- for user questions, please use the email address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here to ensure that you get an answer instead of mystified silence. Is the local resolution map open in addition to the original map? I only see two copies of the same map in the Volume Viewer. Make sure that you open the local resolution map instead of a second copy of the original map. 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 Oct 3, 2025, at 2:07 PM, Roy Chowdhury, Shatabdi wrote: > Hi, > > In the past, I've used chimerax to display local resolution on maps using the tools->volume data->surface color function. In a new map, I'm having difficulty with it. I'm attaching screenshots where the phenix local resolution job suggests the resolution range to be 1.27A - 4.6A range which is in agreement with cryosparc. When I load the cctbx_program.ccp4 file on chimerax, it is unable to color the surface and says the surface values are -0.067 - 0.107. Is there something I should be doing differently? Any suggestions would be deeply appreciated. > > Thanks! > > Shatabdi Roy-Chowdhury, PhD. > Cardiovascular Research Institute > University of California, San Francisco > > _______________________________________________ > Chimera mailing list -- chimera(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-leave(a)cgl.ucsf.edu

1 0

Defining pdb chain ontologies
by Pranav Shah 30 Sep '25

30 Sep '25

Hi Team, I am writing to inquire about the functionality of ChimeraX, specifically concerning multi-subunit complexes with multiple chains of a single protein (e.g., PDB 4v7q). I am wondering if there is a feature that allows for manipulating chains by assigning them to functional ontologies. For instance, with the 4v7q example, I would like to be able to execute commands such as: color #1 "vp4" red `mm #1/"vp4" to #2/"vp4" These ontologies could be grabbed from the cif file and if the user decides define their pwn ontologies/groupings. If such a feature does not exist, would you consider exposing such a feature to the user? 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 4

Orient many tetramers
by Alexandra Zahradnikova 30 Sep '25

30 Sep '25

Hi I have a set of tetramers created by AlphaFold. They are randomly oriented. In order to measure their pore size in a third-party program, I need to orient them with their z axis pointing in the z direction. I can orient them with respect to the screen, but I don't know how to save this view orientation (i.e. so that the z axis in the pdb file goes vertically). Is there any way how to do it? The switch in the "save" command specifying whether to use transformed or untransformed coordinates does not make any difference, and the file is always saved in the original orientation. Best Sasha

3 4

Suggestion for viewdock
by John Irwin 29 Sep '25

29 Sep '25

Hi Team We love viewdock. We would like to suggest allowing hotkeys for adjusting status e.g. for prioritization so that we do not need to mouse all the way down to click to change status. We think this might be a small change with a big usability and productivity impact. Thank you John John Irwin UCSF Pharmaceutical Chemistry http://irwinlab.compbio.ucsf.edu

3 3

Just a Big Thank You
by Esmaeeli,Reza 25 Sep '25

25 Sep '25

Dear ChimeraX Developers, This is Reza and I’m a computational chemist and protein designer. I’ve been a long time user of Chimera and now ChimeraX. Among many visualization programs that I have tried extensively including PyMOL, VMD, Maestro, ChimeraX has remained my favorite. I just wanted to take a moment and write this email just to say thank you for your amazing work. Even though it is free for academic users, this email is the least I should do after so many hours that I have enjoyed using it. The interface is great. The diverse set of features and modules are awesome. And the command line and scripting capabilities are so intuitive and easy to use. Can’t wait to see what comes next. Best Regards, Reza ChimeraX 1.10.1 on macOS Tahoe

4 3

Re: [Chimera-users] Mapping conservation onto a structure
by Elaine Meng 25 Sep '25

25 Sep '25

Hi Shelley! Chimera and ChimeraX are two separate programs, so there are various differences. The email address for ChimeraX questions, chimerax-users(a)cgl.ucsf.edu is CC'd here. I'll answer for ChimeraX since that's what you're using -- ChimeraX has a Sequence Viewer tool which is basically the logical equivalent of Chimera's Multalign Viewer, see: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html> See also the detailed tutorial on using ChimeraX to map conservation from a sequence alignment onto structures: <https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-…> 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 Sep 25, 2025, at 8:36 AM, Shelley Copley via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Has Multalign viewer been taken down? I don’t see it in ChimeraX 1.10. Is there a different way to map sequence conservation onto a structure? > Thanks! > Shelley

2 1

Is there a way to download a pdb and it's associated density map in one command
by Samuel Haysom 24 Sep '25

24 Sep '25

Is there any way I can fetch a pdb file from the web (e.g. $ open 1X2Y) and then also automatically fetch the associated cryoEM map if there is one? Looking in the mmCif file, there is a flag for the associated emdb-map (e.g. in 5ljo the mmCIF file there is a _pdbx_database_related.db_id flag with the corresponding id. It would be useful if this could be added as a flag to the open command if it isn't already. I'm sure it is also possible in some kind of script but I'm not hugely familiar with how to script in chimeraX. 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.

4 3

Ligand center
by NUR AIDA SAKINAH 24 Sep '25

24 Sep '25

Hi ChimeraX teams, I want to search ligand center for docking analysis. What command do I need to use to retrieve the ligand center (x,y,z)? Example pdbid is 4yvv and the ligand is GBM. So i want the GBM's x,y,z coordinates. Thank you. Regards, Aida.

3 2

Regarding the method used by chimeraX for SASA calculation
by Prathvi Singh 23 Sep '25

23 Sep '25

Hi Elaine, I have used NACCESS ( https://www.bioinf.manchester.ac.uk/naccess/nac_intro.html) to calculate the SASA for a protein. It used the Lee & Richards (1971, J. Mol. Biol., 55, 379-400) method to calculate SASA. I wanted to know whether chimeraX also uses the same method to calculate SASA or not. If not, then can you mention how the chimeraX method differs from the method used by NACCESS? Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 2

About "Minimizing Structure" feature in Chimera
by Zheyun Wang (MED,124090655) 23 Sep '25

23 Sep '25

Dear ChimeraX developers: I am Wang Zheyun, a student in Chinese University of Hong Kong, Shenzhen. In my computational biology course, our professor demonstrated to us that the molecular structure (a file containing several water molecules) can be changed to an energy-minimizing structure using "Minimizing structure" function in Chimera. However, I cannot find this function in ChimeraX(1.10.1), and professor told me that these two are completely different softwares. Is this function available in ChimeraX? If so, may I know where it is? If not, will this be added to ChimeraX or is it deliberately deleted? Looking forward to your reply! Sincerely, Wang Zheyun

2 1

Python API: locate_maximum logic
by nrajan53045＠utexas.edu 19 Sep '25

19 Sep '25

Hi there, I was hoping to implement something similar to the rigid rotation/translation optimization within fitmap due to its efficiency. I have some code which appears to implement the same logic as locate_maximum from your github, but is returning wildly different affine matrices than I expect. I just had a couple of questions regarding the logic: 1) locate_maximum receives an conversion matrix from world to voxel space (xyz to ijk) as one of its parameters from volume's matrix_and_transform function. I was wondering what this matrix actually is? I was tracing through the matrix_and_transform function and I couldn't really figure this out. I am currently assuming that the transform matrix is a 3 x 4 affine matrix: 1/v * (I | -O). Where v is the isotropic voxel size, I is a 3 x 3 identity matrix and O is a 3 x 1 vector representing the origin of the map. 2) Within each step of a segment, the following is done (from steps_to_maximum): ``` if step_types: for step in range(steps): calculate_step = step_types[step % len(step_types)] xyz_to_ijk_tf = xyz_to_ijk_transform * move_tf step_tf = calculate_step(points, point_weights, rotation_center, data_array, xyz_to_ijk_tf, ijk_step_size, metric, syminv = syminv, values = values, gradients = gradients) move_tf = move_tf * step_tf ``` In this loop, xyz_to_ijk_transform looks like the full conversion matrix from world to voxel space. But each iteration also multiplies it by move_tf before applying the step calculation, and then updates move_tf again with step_tf. At first glance, it seems like we’re reapplying the same full transform at every step... so why not just apply it once, instead of multiplying it repeatedly inside the loop? And then when we return to locate_maximum, move_tf is once again applied to the full conversion matrix. before continuing the iteration. I apologize if this is nitty gritty detail, but I would really like to make sure my logic is sound when I am implementing my version of this algorithm. Thank you for your time, Nikhil Rajan

2 1

Generate a volume from a shape
by Guillaume Gaullier 18 Sep '25

18 Sep '25

Hello, I am trying to do something seemingly simple, but can't figure out what I am doing wrong. I have an mrc map open as model #1, moved the center of rotation somewhere, then generated a sphere with: shape sphere radius 30 center cofr I got a sphere as model #2, good. Then I want to turn this sphere into a mask, which I try doing like this: volume onemask #2 ongrid #1 At which point I get this error: Expected a density maps specifier or a keyword The documentation of 'volume onemask' says it needs a surface specification as the first argument, and the model panel shows that there is no surface associated to the sphere (then why/how is it displayed? not sure), so that all seems to make sense. And I am stuck at this step: how do I turn this sphere into a surface so I can generate a volume from it? I read the documentation for 'surface', 'volume' and 'shape' but can't find anything to solve this problem. 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

3 3

Guidance on SASA/RSA calculation in ChimeraX
by Kazi Sayeeda 16 Sep '25

16 Sep '25

Dear ChimeraX Support Team, I am currently using ChimeraX (v1.10.1) to study whether certain amino acid residues are surface-exposed or buried in my protein structures (WT and mutants from AlphaFold/NeuroSnap). To assess this, I measured solvent accessible surface area (SASA) with the following commands: measure sasa #1 measure sasa #1:92 measure sasa #1:562 This gives me the following SASA values (in Å²): * WT Ala92: 216.4 Å² * WT Gly562: 189.0 Å² When I compare these to published maximum ASA (MaxASA) values from Tien et al. 2013 (probe radius 1.4 Å): * Ala (max ASA) = 129 Å² * Gly (max ASA) = 104 Å² I get relative solvent accessibility (RSA) values greater than 1: * Ala92: 216.4 / 129 = 1.68 * Gly562: 189.0 / 104 = 1.82 Since RSA should not exceed 1, I believe I am mismatching ChimeraX’s calculation settings with the MaxASA reference set. So my questions are: 1. What radii model and probe radius does measure sasa in ChimeraX use by default? 2. Is there a way in ChimeraX to directly assign per-residue SASA attributes and normalize them internally (so RSA values remain ≤1)? 3. If ChimeraX defaults differ from published MaxASA tables, would you recommend reporting only SASA values, or generating my own MaxASA reference values with ChimeraX for consistency? I would be very grateful for any guidance or documentation pointers so I can report values in a way that is consistent and interpretable. Best, Kazi Sayeeda PhD Candidate Dept. of Cell and Developmental Biology (Krendel Lab) SUNY Upstate Medical University Syracuse, NY 13210 sayeedak(a)upstate.edu<mailto:%20sayeedak@upstate.edu>

2 2

Re: scan results for vr.ucsf.edu
by Tom Goddard 15 Sep '25

15 Sep '25

Hi Greg, The web site report for vr.ucsf.edu <http://vr.ucsf.edu/> you shared takes me to web site that requires a login if I want to see what links are broken. Tom > On Sep 15, 2025, at 6:04 PM, Siteimprove Reports <reports(a)siteimprove.com> wrote: > > > Hi there, > Greg Couch (gregc(a)cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>) wants to share a dashboard report with you. The report was generated from "DCI score dashboard" at 6:02 PM on 9/15/2025. > > View report <https://reports.siteimprove.com/sendnow/8343/c77e8c4c-b3d9-4ba5-b4eb-1c17a3…> > > > > > > > > > > View report <https://reports.siteimprove.com/sendnow/8343/c77e8c4c-b3d9-4ba5-b4eb-1c17a3…> > > © 2025 Siteimprove > Havneholmen 33, DK-1561 Copenhagen, Denmark >

1 0

Display the bfactor value when the mouse goes over a residue?
by Vincent CHAPTAL 15 Sep '25

15 Sep '25

Hello, I'd like to know, in addition to residue name and model, the bfactor of a residue when the mouse goes over it. For example model#1.20/A PHE 1482 bfactor 120.7 Could you help me to do it? Thanks a lot. 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 7

AlphaFold3 structures coloured in ChimeraX
by Vladimir Saudek 12 Sep '25

12 Sep '25

Hello, I am using ChimeraX 10.1 to display the results of AlphaFold3 predictions. I observe a large discrepancy between the colour coding of the quality of the structure (pIDDT) displayed at the output of the AF3 server and ChimeraX (I use the command color bfactor #1 palette AlphaFold, 1 being thenumbero of the structure to colour). ChimeraX's colouring indicates that the quality of the predicted structure is substantially lower then than that of theAF3 server. Is there any possibility to get ChimeraX to display the AF3 server colours? Below is an example, right AF3 output, left ChimedraX. Best regards Vladimir

6 8

Determine an atom-spec from a selection
by Guillaume Gaullier 12 Sep '25

12 Sep '25

Hello chimerax-users, I am comparing different structures that all look mostly identical, and I have to generate figures of some interesting place, but they of course don't all have the same residue numbers and chain IDs (would be too easy...). I managed to work around this problem this way: - open reference structure in which I know the chain IDs and residue numbers I want to look at - open another structure, align it to the reference with mmaker - use 'select zone' with option 'residues true' and an appropriate distance cutoff from the reference structure to select the equivalent residues in the structure under scrutiny: works nicely, I simply have to tweak the distance cutoff interactively depending on how different the current structure is compared to the reference, but it is easier than looking up residue numbers and chain IDs and keeping track of all this different info per structure I am missing one thing: I would like to save these selections as named selections, so I can easily select them again further down in the script. So I need a way to say 'name someName sel' except I can't use that last 'sel' keyword because it is never expanded to the actual atom-spec that would make this trick work, and instead always points to whatever is currently selected. Is there a way to do this? I looked at 'info sel level residue' that prints to the Log something close to what I need (although more than just the atom-spec). Ideally I would like this to work from a command script, so I can automate the generation of the picture of that interesting location from many structures. 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

2 2

High-Resolution images
by Khawar Siddiqui 09 Sep '25

09 Sep '25

Hi Tom, Hope you are fine. Nature Computational Science requires high-resolution VECTOR images like PDF. I noticed that ChimeraX does not have this option. Secondly, I also noticed that images can not be exported with 300-600 dpi Raster files like TIFF or PNG. How shall I proceed? I have no command-line experience. Thanking you in advance. Regards Sohail Dr Khawar Sohail Siddiqui, [cid:8e96f4e1-302e-423d-8433-4bdcdbb4da92]hoo.com This email and any files transmitted with it may contain confidential information. If you believe you have received this email or any of its contents in error, please notify me immediately by return email and destroy this email. Do not use, disseminate, forward, print or copy any contents of an email received in error.

4 4

Re: [EXTERNAL] Question about the software features
by Elaine Meng 09 Sep '25

09 Sep '25

Hi Sepid, There is nothing to map genetic coordinates onto a structure. However, you can show the sequence that goes with your structure (if this is a protein, the amino acid sequence, NOT the DNA) in a separate window and choose residue(s) from there. How do you get the amino acid sequence? Well, you could fetch the corresponding UniProt ID, if you know what it is (e.g. go to uniprot.org <http://uniprot.org/> and search to find it), e.g. command open uniprot:LDLR_HUMAN ... or you can simply show the amino acid sequence directly taken from the structure, e.g. if it is chain B in your structure, command sequence chain /B See the Sequence Viewer documentation for how the sequence and associated structure interact. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.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 Sep 9, 2025, at 3:15 PM, Mazrouee, Sepideh (NIH/OD) [E] <sepid.mazrouee(a)nih.gov> wrote: > > Hi Elaine, > > Thank you for your suggestions. While arbitrary labels could be a workaround, I need a more precise solution. > > I have a list of genetic coordinates for several protein domains generated by another program. Is there a way to map these coordinates onto the ChimeraX GUI? maybe via the “Nucleotide,” “Sequence,” or a related menu option? If I can locate the residues in the structure, I can then apply custom labels you suggested to highlight them. > > I would appreciate your help! > > Best, > Sepid

1 0

Color cartoon transfer
by Михаил Егорочкин 07 Sep '25

07 Sep '25

Hello, my name is Michael. While using ChimeraX, I encountered a problem with transferring colored models. I created a session in Chimera where I loaded several PDB files, applied custom coloring to them, and now I want to combine the colorings from two different sessions. However, I cannot manage to do this. I tried using the .ccm format, but any session save results in a 0-byte file, and I haven’t found a solution yet. Do you have any idea how this issue can be resolved? Best regards, Michael.

2 2

Monitor distance throughout the trajectory
by Alexandra Zahradnikova 05 Sep '25

05 Sep '25

Hi I would like to record the evolution of distance between two atoms along all points of a MD trajectory into a file but I cannot find a command to keep saving/displaying the distance in the log for the whole trajectory, just for individual points (although of course the actual distance is shown in the GUI when the trajectory is played). Thanks in advance for help. Best regards Sasha

3 5

Re: ChimeraX bond rotation with right mouse
by Elaine Meng 05 Sep '25

05 Sep '25

Hello David Ron, For future reference, please use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address CC'd here for asking questions, to ensure you get an answer. Right Mouse tool documentation says you can combine the "bond rotation" mouse mode with Shift key to move the larger side instead of the smaller side. Scroll down to see the "bond rotation" description: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.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 Sep 5, 2025, at 7:00 AM, David Ron <dr360(a)cam.ac.uk> wrote: > > Dear Dr. Meng, > Can you advise on a matter arising in ChimeraX [version 1.10 (2025-06-26)] > When using the right-mouse option to rotate a bond, is there an option to specify which part of the model moves and which part stays in place? > ChimeraX’s default seems set (intelligently enough) to rotate the portion of the model with the smallest mass (the fewest atoms), but sometimes it is convenient to be able to use then right mouse to rotate the bulkier part of the model, leaving the less bulky part in place. > Can this be achieved? > [I am aware of the option of using the command line to specify torsion angle about a dihedral (and which parts of the model moves), but this requires entering a specific angle of rotation and thus lacks the kind of fine control afforded by the right mouse bond rotation feature]. > Thanks for considering. > Sincerely, > David Ron > Cambridge Institute for Medical Research > University of Cambridge > Keith Peters Building > Addenbrookes Hospital > Cambridge CB2 0XY > United Kingdom > Office: +44 1223 768 940 > Mobile: +44 7941 015 666 > Email: dr360(a)cam.ac.uk

2 1

ChimeraX 1.8 user manual
by NUR SYAMIM SYAHIRAH MAT HUSSIN 04 Sep '25

04 Sep '25

Hi, I am a new user. I am working on aptamer design. The target is animal protein. However, I am not very capable of using ChimeraX to view my aptamer-binding (after finishing docking). Can I get any tips, manuals, or video demonstrations that relate to the study? Regards PENAFIAN: E-mel ini dan apa-apa fail yang dihantar bersama-samanya ("Mesej") adalah dihasratkan hanya untuk kegunaan penerima yang dinyatakan di atas dan mungkin mengandungi maklumat yang tidak umum, bermilik, istimewa, sulit dan dikecualikan dari penzahiran di bawah undang-undang yang terpakai termasuklah Akta Rahsia Rasmi 1972. BACA SELANJUTNYA... <https://mail.uitm.edu.my/disclaimer> DISCLAIMER : This e-mail and any files transmitted with it ("Message") is intended only for the use of the recipient(s) named above and may contain information that is non-public, proprietary, privileged, confidential and exempt from disclosure under applicable law including the Official Secrets Act 1972. READ MORE... <https://mail.uitm.edu.my/disclaimer>

2 1

Hide missing residues label
by colin＠gauvin.id 04 Sep '25

04 Sep '25

Hello all, If there are a number of missing residues, sometimes there is a label such as "16 residues" at the dashed line where they would be. Is there a way to hide this for figure making? For the life of me, I cannot figure it out. Best, Colin

2 1

residues labels not showing; no error in the log
by Krishnan Raman 04 Sep '25

04 Sep '25

[cid:image001.png@01DC1DA9.88EDB2F0] Residue labels not showing up with no error in the log! I am sure iam missing something. Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals 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

Cylindrical averaging for radial density profiles
by Dmitry Semchonok 04 Sep '25

04 Sep '25

Dear Colleagues, I need to perform cylindrical averaging of membrane protein density maps (MRC files) to generate radial density profiles for membrane thickness analysis. Does ChimeraX have built-in functionality for this, or are there existing scripts/plugins available? If not, could you provide guidance on the best approach to implement this? Thank you! Kind regards, Dmitry

2 3

How to apply selected graphics JUST to the side chain and not the backbone?
by mfmccl＠berkeley.edu 02 Sep '25

02 Sep '25

Hello all! I can't seem to figure out how to apply selected graphics to give a silhouette on residues of interest without it adding a silhouette to the side chain and the respective backbone cartoon. Is it possible to just select the sidechain atoms only? I've tried my usual tricks but can't seem to get it to work. I've tried "cartoon suppress true" & selecting the individual atoms of the sidechain but it always also selects the cartoon backbone. Thanks! Madi

2 2

Minimize structure capability in chimeraX?
by Kabir Gupta 02 Sep '25

02 Sep '25

Hi all, Does ChimeraX currently have the capability to minimize a structure? The functionality I'm talking about is of the sort available under Tools -> Structure Editing -> Minimize Structure... in the original Chimera. Last I can find is from a mail thread in 2020, at which point this had not yet been implemented in ChimeraX. Is there an acceptable substitute to achieve the same thing now, or do I have to reopen in original Chimera to do minimizations? Thanks very much, Kabir

2 2

An issue with Boltz-2 in ChimeraX daily
by Enrico Martinez 02 Sep '25

02 Sep '25

Dear ChimeraX users! I am testing the Boltz-2 on Mac in the ChimeraX-daily: for one receptor (provided fasta sequence) and 5 ligands (provided smiles strings for each compound). My calculations are running on GPUs and I see the Boltz-2 folder with the results. However, the ChimeraX send the following error message (copied directly from log): Running Boltz prediction of 5 ligands on gpu Using cached multiple sequence alignment Running boltz prediction failed with exit code 1: command: /Users/enrico/boltz22/bin/boltz predict /Users/enrico/Desktop/boltz_2 --accelerator gpu --no_kernels stdout: Boltz version 2.2.0 Checking input data. Processing 5 inputs with 5 threads. Running structure prediction for 5 inputs. Predicting: | | 0/? [00:00<?, ?it/s] Predicting: 0%| | 0/5 [00:00<?, ?it/s] Predicting DataLoader 0: 0%| | 0/5 [00:00<?, ?it/s] Predicting DataLoader 0: 20%|██ | 1/5 [01:55<07:42, 0.01it/s] Predicting DataLoader 0: 40%|████ | 2/5 [03:55<05:53, 0.01it/s] Predicting DataLoader 0: 60%|██████ | 3/5 [05:53<03:55, 0.01it/s] Predicting DataLoader 0: 80%|████████ | 4/5 [07:56<01:59, 0.01it/s] Predicting DataLoader 0: 100%|██████████| 5/5 [09:59<00:00, 0.01it/s]Number of failed examples: 0 Predicting DataLoader 0: 100%|██████████| 5/5 [09:59<00:00, 0.01it/s] Predicting property: affinity Checking input data for affinity. Running affinity prediction for 5 inputs. stderr: 0%| | 0/5 [00:00<?, ?it/s] 20%|██ | 1/5 [00:05<00:23, 5.78s/it] 100%|██████████| 5/5 [00:05<00:00, 1.17s/it] GPU available: True (mps), used: True TPU available: False, using: 0 TPU cores HPU available: False, using: 0 HPUs /Users/enrico/boltz22/lib/python3.11/site-packages/pytorch_lightning/trainer/connectors/logger_connector/logger_connector.py:76: Starting from v1.9.0, `tensorboardX` has been removed as a dependency of the `pytorch_lightning` package, due to potential conflicts with other packages in the ML ecosystem. For this reason, `logger=True` will use `CSVLogger` as the default logger, unless the `tensorboard` or `tensorboardX` packages are found. Please `pip install lightning[extra]` or one of them to enable TensorBoard support by default Mon Sep 1 14:38:24 2025: Loading Boltz structure prediction weights /Users/enrico/boltz22/lib/python3.11/site-packages/pytorch_lightning/utilities/migration/utils.py:56: The loaded checkpoint was produced with Lightning v2.5.0.post0, which is newer than your current Lightning version: v2.5.0 Mon Sep 1 14:38:35 2025: Finished loading Boltz structure prediction weights Mon Sep 1 14:38:35 2025: Starting structure inference /Users/enrico/boltz22/lib/python3.11/site-packages/pytorch_lightning/trainer/connectors/data_connector.py:420: Consider setting `persistent_workers=True` in 'predict_dataloader' to speed up the dataloader worker initialization. /Users/enrico/boltz22/lib/python3.11/site-packages/torch/utils/data/dataloader.py:684: UserWarning: 'pin_memory' argument is set as true but not supported on MPS now, then device pinned memory won't be used. warnings.warn(warn_msg) Mon Sep 1 14:38:44 2025: Begin structure inference ligand4 (1 of 5) /Users/enrico/boltz22/lib/python3.11/site-packages/boltz/model/loss/diffusionv2.py:51: UserWarning: The operator 'aten::linalg_svd' is not currently supported on the MPS backend and will fall back to run on the CPU. This may have performance implications. (Triggered internally at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/mps/MPSFallback.mm:15.) U, S, V = torch.linalg.svd( Mon Sep 1 14:40:40 2025: End structure inference ligand4 (1 of 5) Mon Sep 1 14:40:40 2025: Begin structure inference ligand5 (2 of 5) Mon Sep 1 14:42:40 2025: End structure inference ligand5 (2 of 5) Mon Sep 1 14:42:40 2025: Begin structure inference ligand2 (3 of 5) Mon Sep 1 14:44:38 2025: End structure inference ligand2 (3 of 5) Mon Sep 1 14:44:38 2025: Begin structure inference ligand3 (4 of 5) Mon Sep 1 14:46:41 2025: End structure inference ligand3 (4 of 5) Mon Sep 1 14:46:41 2025: Begin structure inference ligand1 (5 of 5) Mon Sep 1 14:48:44 2025: End structure inference ligand1 (5 of 5) Mon Sep 1 14:48:57 2025: Finished structure inference Mon Sep 1 14:48:57 2025: Loading affinity prediction weights Traceback (most recent call last): File "/Users/enrico/boltz22/bin/boltz", line 8, in <module> sys.exit(cli()) ^^^^^ File "/Users/enrico/boltz22/lib/python3.11/site-packages/click/core.py", line 1157, in __call__ return self.main(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/enrico/boltz22/lib/python3.11/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/Users/enrico/boltz22/lib/python3.11/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/enrico/boltz22/lib/python3.11/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/enrico/boltz22/lib/python3.11/site-packages/click/core.py", line 783, in invoke return __callback(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/enrico/boltz22/lib/python3.11/site-packages/boltz/main.py", line 1419, in predict model_module = Boltz2.load_from_checkpoint( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/enrico/boltz22/lib/python3.11/site-packages/pytorch_lightning/utilities/model_helpers.py", line 125, in wrapper return self.method(cls, *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/enrico/boltz22/lib/python3.11/site-packages/pytorch_lightning/core/module.py", line 1581, in load_from_checkpoint loaded = _load_from_checkpoint( ^^^^^^^^^^^^^^^^^^^^^^ File "/Users/enrico/boltz22/lib/python3.11/site-packages/pytorch_lightning/core/saving.py", line 63, in _load_from_checkpoint checkpoint = pl_load(checkpoint_path, map_location=map_location) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/enrico/boltz22/lib/python3.11/site-packages/lightning_fabric/utilities/cloud_io.py", line 60, in _load return torch.load( ^^^^^^^^^^^ File "/Users/enrico/boltz22/lib/python3.11/site-packages/torch/serialization.py", line 1491, in load with _open_zipfile_reader(opened_file) as opened_zipfile: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/enrico/boltz22/lib/python3.11/site-packages/torch/serialization.py", line 771, in __init__ super().__init__(torch._C.PyTorchFileReader(name_or_buffer)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ RuntimeError: PytorchStreamReader failed reading zip archive: failed finding central directory Could you precise which package causes this issue and how would the problem be solved in the ChimeraX update? Many thanks for help!! Enrico

2 4

Boltz-2 in ChimeraX daily
by Enrico Martinez 02 Sep '25

02 Sep '25

Dear ChimeraX users! I am testing the Boltz-2 on Mac in the ChimeraX-daily: for one receptor (provided fasta sequence) and 5 ligands (provided smiles strings for each compound). My calculations are running on GPUs and I see the Boltz-2 folder with the results. However, the ChimeraX send the following error message (coppied directly from log):

1 0