- ChimeraX-users - RBVI Mailing Lists

displaying pLDDT in same color as Alphafold server?
by Nakamura, Toru 29 May '26

29 May '26

Hello, I am not sure if this is the right place to ask, but I have tried and failed Chimera to display what resembles the AlphaFold server, and it seems that it is using a long color scheme. I typed “color factor #1 palette alphafold, but it does nothing, and the predicted aligned error & what is displayed is probably a different color scheme? What am I missing here? Thank you for your help! Toru [Screenshot 2026-05-29 at 6.30.14 AM.png][Screenshot 2026-05-29 at 6.30.45 AM.png] ==================================== Toru M. Nakamura, Ph.D. Professor of Biochemistry & Molecular Genetics ~~~~~~~~~~~~~~~~~~~~~~~~~~ University of Illinois at Chicago College of Medicine Dept. of Biochem. & Mol. Genet. 900 S. Ashland Ave. MBRB Room 2202, MC669 Chicago IL 60607, USA ~~~~~~~~~~~~~~~~~~~~~~~~~~ E-MAIL: nakamut(a)uic.edu Lab: https://nakamura.lab.uic.edu/

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Security scan complaining about ChimeraX Python component
by Kirshner, Dan 27 May '26

27 May '26

Hello: Sorry, we’ve got an annoying security scan. Here’s its complaint: Path : /Applications/ChimeraX-1.12-rc2026.05.23.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/aiohttp-3.13.1.dist-info Installed version : 3.13.1 Fixed version : 3.13.4 Potential Vulnerability : Component Is there some way for me to update the Python that ChimeraX uses? Thanks very much, —Dan

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regional minimization?
by Daniel David Richman 27 May '26

27 May '26

Hi folks, In Maestro there’s a “minimize” feature where only the selected atoms are allowed to move. It’s very helpful when I make a mutation that I want to locally relax and I want to be sure that the rest of the system won't change. Does ChimeraX support anything like this, or is it on the horizon? Thanks, Daniel

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Cellpack reading
by huybk81＠gmail.com 22 May '26

22 May '26

Hi, In Chimera, there is a cellpack plugin to open a cellpack file. Is there any particular reason that ChimeraX doesn't have an equivalent function?

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fitmap - search flipped map?
by Oliver Clarke 19 May '26

19 May '26

Hi, I would like to suggest a possible enhancement for fitmap that would be useful in cryoEM workflows - optionally searching both the original map, and a z-flipped copy. In cryoEM, we often obtain initial reconstructions using ab initio reconstruction, which may converge on either the correct or inverted hands, and at low resolution, it is sometimes difficult to distinguish which (if any) is a correct solution - often, unambiguous fit of an atomic model is helpful to confirm that one has a correct solution. Fitmap with global search (e.g. fitmap #1 in #2 search 100 radius 5) is useful to get an initial fit list. It would therefore be convenient if fitmap had an option to automatically test the fit of a model vs both the selected map and a z-flipped copy. We do this now by pre-flipping the map and doing two searches (one against each copy), but when all the classes are loaded from a classification job this can become a bit unwieldy, in terms of keeping track of which map ID corresponds to the flipped copy of which map. Cheers Oli

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Does ChimeraX incorporate bond geometry or torsional state into atom display?
by Wes Dennis 19 May '26

19 May '26

Hi, My nameis Wes Dennis and I am a retired Geophysicist who is just interested in stuff. I am trying to understand what I am seeing with two ChimeraX images. I applied identical atom-name based coloring commands to the same residue range in two different crystal structures of the same molecule — backbone atoms colored blue, aromatic base atoms colored yellow. The visual result is strikingly different between the two structures. In one, blue color appears to spread into the base panels — a structure in which torsional stresses are present. In the other, where torsional stresses are absent, the base panels are clean yellow with no blue intrusion. My question: does ChimeraX incorporate any geometry-dependent information — bond angles, torsional state, idatm type reassignment based on local environment — into atom rendering or classification that would cause identical coloring commands to produce visually different results across structures? Or is ChimeraX rendering purely atomic positions as recorded in the mmCIF file with no geometry-based modification? Two Images attached Thank you for your help Wes Dennis ------------------------------

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Fwd: opening cryoEM SPA maps using "volume" view mode
by Eric Pettersen 19 May '26

19 May '26

> Begin forwarded message: > > From: Jonathan Paul Remis <jpremis(a)berkeley.edu> > Subject: opening cryoEM SPA maps using "volume" view mode > Date: May 18, 2026 at 4:36:10 PM PDT > To: chimerax-bugs(a)cgl.ucsf.edu > > Hello wonderful people that build and maintain Chimera! > > > I have run into a bit of an odd observation which when compounded with some basic biochemistry has left me scratching my head. Essentially, when I open one of our SPA volumes in chimerax and choos "volume" in the volume viewer I am able to see a single bright spot in the volume. If I process our data with C2 symmetry we see two bright spots. > > I had thought this was biologically relevant but I opened up a couple more structures from our lab and other labs and see this is pretty common. Please see the attached images and you can see ApoFerritin has 24 bright spots, and Aldolase has 4. > > In the case of my sample - hemoglobin - the bright spot co-localizes with a iron element in the structure. I want to believe this has something to do with the density/scattering of the Fe but am at a loss for why we would not see 4 of them. Hemoglobin has 4 heme centers and 4 Fe atoms. > > Thank you in advance for any suggestions or support you can provide. > > Thanks, > Remis > > > > > > > > > > > -- > Jonathan Remis > Scientific Engineer > Müller Lab > University of California, Berkeley

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pdb file problems and chimerx
by Steven Brawer 15 May '26

15 May '26

I will be using ChimeraX much more extensively this fall, and I think the answer to the question below might be useful (and not just for me). Does there exist some list (or lists) of common pdb file errors? One probably can't cover all possibilities, but perhaps there are some common ones that one could find automatically by writing a python program to examine the file. (Perhaps some programs already exist.) Recently there was a case of misplaced spaces and also of duplicated lines. Presumably one could (perhaps) add a search for the correct number of atoms in each residue. What about the existence/presence of water or heavy ions? Perhaps searching for unexpected atom-atom-atom angles or bond lengths (or even separations)? Perhaps an AI agent might be trained? Thanks Steve Brawer

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Covalently attaching unusual ligands
by TheWildBynapie 15 May '26

15 May '26

Hi there, I'm a bioinformatics UCT student and we've been given an assignment to solve a protein structure. Everyone has been struggling with this step and I've tried many many ways to get this to work in ChimeraX, but I get new errors every time so I'm asking for help. Sorry for the long question, but I would *highly* appreciate help at this point (and so would my class - so if I get an answer you'll be making ~30 people very happy, not just 1!) Essentially this ligand has a sulphur that makes a thioester to Cys 146, our professor said we should remove the Cys sulphur and then combine the ligand and the remainder of the ligand into one residue and name it 'AKG.' We have a dimer so we also do this in 2 places. We need to refine this using ISOLDE, which is where most of my problems appear. Then he says we can use 'AKG.xml' in residue parameterisation so ISOLDE will accept our residue. Currently the way my pdb is layed out causes chimera to only render the ligand part of AKG but not the Cys part. I don't know why, and more importantly my general understanding of how ChimeraX reads pdb files is lacking. *So I suppose finally my actual question*: what do I need to do to make it so ChimeraX renders the residue correctly, and ISOLDE accepts AKG.xml and can actually run a simulation on this pdb? I've attached: 1: AKG.xml (for residue parameterisation) 2: 5 - refine1.mtz (the electron density map data) 3: 6c - part of AKG missing.pdb (the current pdb I'm working with where the Cys part of residue 146 isn't rendered) 4: 6b - pre-covalent linking.pdb (the latest copy of the pdb I could get running in ISOLDE simulations. This has the protein dimer and 2 ligands as 3 separate models. I'd already deleted the Cys's Sulphur here so it's more like an Ala in this case) Sorry for such a massive email, but I wanted to be as specific as possible with my problem. If you could provide me some help it would be extremely helpful. Sadly our lectures for this module are over and getting our lecturer to explain anything is virtually impossible. Thanks so much, Byron (and the rest of my class to be honest)

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Can you export results of your work in Chimera as a pdb file
by Vojo P Deretic 13 May '26

13 May '26

Can you export results of your work in Chimera (for example after matching and aligning structure) as a .pdb file? Vojo Deretic, Ph.D. Distinguished Professor Department Chair, MGM Director, AIM Center University of New Mexico School of Medicine vderetic(a)salud.unm.edu<mailto:vderetic@salud.unm.edu> Follow AIM, NIH-funded Center of Biomedical Research Excellence: https://www.autophagy.center/ X/Twitter @AIM_autophagy Don’t forget to acknowledge the AIM Center (Autophagy, Inflammation and Metabolism) and the CoBRE grant in publications The AIM Center is supported by NIH grant P20GM121176. For citation options see suggested wording at https://www.autophagy.center/

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Re: Error using Boltz in Windows 11 with himeraX 1.11.1
by Tom Goddard 13 May '26

13 May '26

Hi Trevor, I updated the ChimeraX 1.12 release candidate and daily builds so that Boltz and OpenFold installation will use PyTorch for CUDA 12.8 which works with Nvidia Blackwell architecture GPUs such as Nvidia RTX 5080. ChimeraX builds dated May 14, 2026 or newer will use this. It is fine if your computer has a newer CUDA version (e.g. 13.0). The change just effects which CUDA API PyTorch tries to use and it will work with CUDA 12.8 or newer. Tom

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nucleotide tube/slab or slab for modified nucleotides
by Daniel Larsson 13 May '26

13 May '26

Is it possible to show modified nucleotides as tube/slab or slab? Some common modified residues are recognized as nucleotides, such as PSU, but not e.g. 2MA or 2MG (present in e.g. PDB 7K00)? ChatGPT suggested to rename the residues or redefine the polymer type, but these tricks do not work. Regards, Daniel 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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Difficulty for installing isolde in chimeraX 1.11.1
by Subrata Duary cy20d750 13 May '26

13 May '26

Hi, I have downloaded isolde for refinement of cryo-EM maps using isolde. But, I cannot open the downloaded file for integrating isolde. Photo attached below. How to resolve this issue ? Thank you Subrata [image: image.png]

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Match align in chimerax
by Charles 11 May '26

11 May '26

Hello, I am curious if the Match > align tool has been implemented yet in chimerax? I do not see it in any of the tools and using the command line msa3d nor matchmaker #1 to #2 startMatchAlign seems to be working. I can do it manually by aligning each structure individually by chain or by aligning the chains that i know match each other using the pair ss function with matchmaker. i found an old thread that said it was submitted as ticket #7359 but no other updates besides that. Thank you, Charles

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Error using Boltz in Windows 11 with himeraX 1.11.1
by trevor SEWELL 08 May '26

08 May '26

How do I remedy the following error with Boltz predictions on a Windows 11 system with ChimeraX 1.11.1 I have tried Cuda 13.2 and Cuda 12.8 I am not sufficiently skilful to obey the following instructions: NVIDIA GeForce RTX 5080 Laptop GPU with CUDA capability sm_120 is not compatible with the current PyTorch installation. The current PyTorch install supports CUDA capabilities sm_50 sm_60 sm_61 sm_70 sm_75 sm_80 sm_86 sm_90. If you want to use the NVIDIA GeForce RTX 5080 Laptop GPU GPU with PyTorch, please check the instructions at https://pytorch.org/get-started/locally/ Many thanks for your kind help! All the best Trevor Running boltz prediction failed with exit code 1: command: C:\Users\sewel/boltz22\Scripts\boltz.exe predict C:\Users\sewel/Desktop/boltz_omega_amidase\omega_amidase.yaml --accelerator gpu --no_kernels stdout: Boltz version 2.2.0 Checking input data. Processing 1 inputs with 1 threads. Running structure prediction for 1 input. stderr: 0%| | 0/1 [00:00Using bfloat16 Automatic Mixed Precision (AMP) GPU available: True (cuda), used: True TPU available: False, using: 0 TPU cores HPU available: False, using: 0 HPUs C:\Users\sewel\boltz22\Lib\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 Fri May 8 10:27:30 2026: Loading Boltz structure prediction weights C:\Users\sewel\boltz22\Lib\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 Fri May 8 10:28:00 2026: Finished loading Boltz structure prediction weights Fri May 8 10:28:00 2026: Starting structure inference C:\Users\sewel\boltz22\Lib\site-packages\torch\cuda\_init_.py:287: UserWarning: NVIDIA GeForce RTX 5080 Laptop GPU with CUDA capability sm_120 is not compatible with the current PyTorch installation. The current PyTorch install supports CUDA capabilities sm_50 sm_60 sm_61 sm_70 sm_75 sm_80 sm_86 sm_90. If you want to use the NVIDIA GeForce RTX 5080 Laptop GPU GPU with PyTorch, please check the instructions at https://pytorch.org/get-started/locally/ warnings.warn( You are using a CUDA device ('NVIDIA GeForce RTX 5080 Laptop GPU') that has Tensor Cores. To properly utilize them, you should set ⁠ torch.set_float32_matmul_precision('medium' | 'high') ⁠ which will trade-off precision for performance. For more details, read https://pytorch.org/docs/stable/generated/torch.set_float32_matmul_precisio… LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [0] C:\Users\sewel\boltz22\Lib\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. Traceback (most recent call last): File "C:\Users\sewel\boltz22\Lib\site-packages\pytorch_lightning\trainer\call.py", line 47, in _call_and_handle_interrupt return trainer_fn(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\sewel\boltz22\Lib\site-packages\pytorch_lightning\trainer\trainer.py", line 898, in _predict_impl results = self._run(model, ckpt_path=ckpt_path) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\sewel\boltz22\Lib\site-packages\pytorch_lightning\trainer\trainer.py", line 982, in _run results = self._run_stage() ^^^^^^^^^^^^^^^^^ File "C:\Users\sewel\boltz22\Lib\site-packages\pytorch_lightning\trainer\trainer.py", line 1021, in _run_stage return self.predict_loop.run() ^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\sewel\boltz22\Lib\site-packages\pytorch_lightning\loops\utilities.py", line 179, in _decorator return loop_run(self, *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\sewel\boltz22\Lib\site-packages\pytorch_lightning\loops\prediction_loop.py", line 105, in run self.setup_data() File "C:\Users\sewel\boltz22\Lib\site-packages\pytorch_lightning\loops\prediction_loop.py", line 162, in setup_data length = len(dl) if has_len_all_ranks(dl, trainer.strategy, allow_zero_length) else float("inf") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\sewel\boltz22\Lib\site-packages\pytorch_lightning\utilities\data.py", line 105, in has_len_all_ranks if total_length == 0: ^^^^^^^^^^^^^^^^^ RuntimeError: CUDA error: no kernel image is available for execution on the device CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. For debugging consider passing CUDA_LAUNCH_BLOCKING=1 Compile with ⁠ TORCH_USE_CUDA_DSA ⁠ to enable device-side assertions. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "", line 198, in _run_module_as_main File "", line 88, in _run_code File "C:\Users\sewel\boltz22\Scripts\boltz.exe\_main_.py", line 7, in File "C:\Users\sewel\boltz22\Lib\site-packages\click\core.py", line 1157, in _call_ return self.main(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\sewel\boltz22\Lib\site-packages\click\core.py", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "C:\Users\sewel\boltz22\Lib\site-packages\click\core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\sewel\boltz22\Lib\site-packages\click\core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\sewel\boltz22\Lib\site-packages\click\core.py", line 783, in invoke return __callback(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\sewel\boltz22\Lib\site-packages\boltz\main.py", line 1355, in predict trainer.predict( File "C:\Users\sewel\boltz22\Lib\site-packages\pytorch_lightning\trainer\trainer.py", line 859, in predict return call._call_and_handle_interrupt( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\sewel\boltz22\Lib\site-packages\pytorch_lightning\trainer\call.py", line 68, in _call_and_handle_interrupt trainer._teardown() File "C:\Users\sewel\boltz22\Lib\site-packages\pytorch_lightning\trainer\trainer.py", line 1005, in _teardown self.strategy.teardown() File "C:\Users\sewel\boltz22\Lib\site-packages\pytorch_lightning\strategies\strategy.py", line 536, in teardown self.lightning_module.cpu() File "C:\Users\sewel\boltz22\Lib\site-packages\lightning_fabric\utilities\device_dtype_mixin.py", line 82, in cpu return super().cpu() ^^^^^^^^^^^^^ File "C:\Users\sewel\boltz22\Lib\site-packages\torch\nn\modules\module.py", line 1133, in cpu return self._apply(lambda t: t.cpu()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\sewel\boltz22\Lib\site-packages\torch\nn\modules\module.py", line 915, in _apply module._apply(fn) File "C:\Users\sewel\boltz22\Lib\site-packages\torchmetrics\metric.py", line 907, in _apply _dummy_tensor = fn(torch.zeros(1, device=self.device)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ RuntimeError: CUDA error: no kernel image is available for execution on the device CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. For debugging consider passing CUDA_LAUNCH_BLOCKING=1 Compile with ⁠ TORCH_USE_CUDA_DSA ⁠ to enable device-side assertions.

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Question about fitting
by Wendy Lera 07 May '26

07 May '26

Hello, I have made the perfect fit between a map and model. However, the center is not well aligned and I can not repeat it in several layers. Check the images and the command used..how can I make this work?[image: Screenshot 2026-04-24 at 09.36.41.png] [image: Screenshot 2026-05-06 at 15.04.18.png]

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Question about displaying backbone atoms as sticks while maintaining cartoon representation
by Eulberg, Tobias 04 May '26

04 May '26

Dear ChimeraX Development Team, I am working on visualizing the oxyanion hole in an alpha/beta hydrolase structure and have encountered a display issue that I hope you can help me resolve. What I'm trying to achieve: I would like to display the backbone atoms (N, CA, C, O, and amide H) of specific residues (residues 36 and 103) as sticks to highlight the oxyanion hole NH groups, while maintaining the cartoon representation for the entire protein including these residues. The problem: When I display both the cartoon and the backbone atoms as sticks for the same residues, ChimeraX creates conical/tapered transitions connecting the cartoon ribbon to the displayed atoms. These conical shapes obscure the backbone atoms I'm trying to highlight, particularly the amide NH groups that form the oxyanion hole. My question: Is there a way to display backbone atoms as sticks for specific residues while maintaining the cartoon representation for those same residues, without the conical transition artifacts? Alternatively, is there a recommended workflow for highlighting specific backbone atoms (particularly amide NH groups) in the context of a cartoon representation without visual interference? I've attached a screenshot showing the conical transitions that appear when both representations are active. Thank you for your time, any guidance would be greatly appreciated. Best regards, Tobias Eulberg Tobias Eulberg M. Sc. Doktorand PhD student Technische Universität Berlin Fakultät II - Mathematik und Naturwissenschaften Institut für Chemie Faculty II - Mathematics and Natural Sciences Department of Chemistry Müller-Breslau-Str. 10, Room L302, 10623 Berlin GERMANY Tel.: +49 (0)30 314-28718<tel:+49%2030%20314%2028718> tobias.eulberg(a)chem.tu-berlin.de<mailto:tobias.eulberg@chem.tu-berlin.de> www.tu.berlin/biochemie<http://www.tu.berlin/biochemie>

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Error in AlphaFold
by Chang, Ju Fang 30 Apr '26

30 Apr '26

Hi, There, I think there might be a version compatibility issue, could you please help? Thank you Jufang ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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masking partial xplor volumes in ChimeraX
by Jan Hofmann 30 Apr '26

30 Apr '26

Hello, I am overlaying electron densities from xplor files with .pdb structures. The problem is that the .xplor files only crop along X, Y and Z with the vop cover # fbox command. Is there any command or option to hide some of the xplor densities, but not all? I have a screenshot attached and would like to hide the density volume circled. If not, can xplor files be converted into a different file type that allows that? Thank you. Best, *Jan Hofmann, M.Sc.* *PhD Candidate, Department of Chemistry* *Chapman Group* Stony Brook University *jan.hofmann(a)stonybrook.edu <andrew.nicoll(a)stonybrook.edu>* Office: Room 577, Chemistry [image: image.png]

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Opening mol2 files with ChimeraX without ViewDock windows
by Ute Roehrig 30 Apr '26

30 Apr '26

Dear Developers, Is it possible to change the default behavior of ChimeraX when opening files in mol2 format to not showing the ViewDock window? I know I can add "showtool false" on the command line or make an alias, but I often open multiple mol2 files directly from the linux command line (chimerax *.mol2), and then the screen becomes cluttered with ViewDock windows. Alternatively, is there a command to close all opened ViewDock windows? Thank you for your help, Ute

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collapse atom-atom pbonds into residue-residue contacts
by Weiskopf, Erika Nicole 28 Apr '26

28 Apr '26

Hello, I want to visualize atom-atom pbonds (generated through the contacts feature) as single residue-residue contacts. Is there a way to do this and/or a way to delete single pbonds I have selected to manually clean up the image? Thanks, Erika The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Question about openfold command line syntax
by David S. Fay 27 Apr '26

27 Apr '26

Hi, I couldn’t find documentation regarding the correct syntax for running multiple models and using different seeds from the ChimeraX openfold platform. I tried something similar to what has worked for boltz: openfold predict #1/A #1/B recycle 3 seed 3 samples 5, but got an error (Expected a keyword). Tried a few other iterations but came up empty. Thanks in advance. David Fay

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Angle between an axis and a plane
by Alexandra Zahradnikova 24 Apr '26

24 Apr '26

Dear All, I am trying to calculate a set of angles between pairs of axes and planes. Example: sel #1/B:348,1052 @ca; define axis sel; sel #1:1052 @ca; define plane sel; angle #1.3 #1.4 My problem is that the angle is always reported positive, no matter whether the axis goes "up" or "down" from the plane, when "up" and "down" are defined relative to the orientation of the molecule. Is there any way how to distinguish between these two cases automatically? Thanks very much in advance. Best regards Sasha Zahradnikova

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Protein-protein interactions assessed through Boltz using ChimeraX consistently scoring quite low
by David S. Fay 23 Apr '26

23 Apr '26

Greetings, We’ve been working with largish data sets and testing for protein-protein interactions using AF2, AF3 and Boltz. For many of these tests we’ve run the prediction programs locally on our supercomputer. We’ve also done a good amount of primary testing and double-checking using web-based interfaces available for CoLab(AF2) and AF3. I just recently started using Boltz2 through the ChimeraX interface. What I’ve noticed so far is a pattern where the Boltz prediction through ChimeraX is giving much lower interaction scores, based on ipTM and PAEs, than Boltz through our supercomputer as well as AF2 and AF3 through our super computer or via the web. I’ve tried running multiple models, seeds, and increasing recycles to 3 as well as checking the two different boxes (Use steering potential vs. Use MSA cache). The commands I’ve run might look like: boltz predict #1/A #1/B recycle 3 seed 4 samples 5. In any case, I’m puzzled as to why the scores are consistently lower. I recognize that I may be doing something wrong. For example, I seem to need to start out by running a first round of Boltz using the interaction window. Then once I get the first prediction, I can next invoke the “boltz predict” as above using different parameters on the command line. (These parameters are not part of the menus in the Boltz window that I can find.) The different runs, seeds, and models, I’m getting do give slightly different results, but they all seem to be under predicting what we know to be are quite strong interactions. I should say that we also see some differences between local and web-based AF3 and AF2 results, but they aren’t as extreme as what we’re seeing from Boltz from what we can tell. Any thoughts? Thanks greatly in advance! David David S. Fay Ph.D. Professor, Department of Molecular Biology Director (PD/PI), National Institutes of Health Wyoming INBRE University of Wyoming email: davidfay(a)uwyo.edu

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ChimeraX download mirror is down
by Elvio Rodriguez Araya 23 Apr '26

23 Apr '26

Hello, I am about to teach a course in structural bioinformatics, and the first step is to download ChimeraX 1.11.1, but the download link is dead. Basically, the course would be suspended if the link doesn't work. Is there any chance for you to share at least the EXE file with me? Sorry for the inconvenience Regards, Elvio -- Dr. Elvio Rodríguez Araya Facultad de Ciencias Bioquímicas y Farmacéuticas, UNR Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET) Suipacha 590, Rosario, Argentina

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Suggestion
by Samo Lešnik 23 Apr '26

23 Apr '26

Dear developers, I have a small suggestion: if the residue name is detected as HOH, TIP3, WAT, ... (whatever the list of waters are), then the bond between H2 and H1 is not drawn, as this is an artifact of the small distance. Best regards, Samo

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New feature request: "shortCircuit" option for clashes command to terminate as soon as single clash is found
by Jon David 22 Apr '26

22 Apr '26

Hi team, I'd like to request new functionality for the clashes command. Specifically, I'd like to request for a new option called "shortCircuit that accepts a Boolean value: True or False. If True, then as soon as any clash is detected, the clashes command terminates; False, then behave the way it does now. For my particular use case, I am making collision checks between pairs of molecule configurations, thousands of pairs. The problem is the more clashes there are, the longer it takes for the clashes command to finish. This is a problem when I'm checking for collisions thousands of times. To have a feature where the clashes command exits early, as soon as it finds ANY clash/collision, would be extremely useful for my case. Thanks, --J

2 3

Ribbon diagram depiction
by Das, Abhinaba 22 Apr '26

22 Apr '26

Hi all, Is it possible to thread a ribbon along non-canonical peptide backbone based helical structure? I was working with CCDC-633286, left is what depicted in the journal article and right is the default view in ChimeraX Thanks, Abhi [cid:3c356f41-2360-426f-86b1-cd758aeca1b0][cid:ae8b49a1-cf5c-4262-9120-dcbb984645b3]

2 1

ChimeraX 1.11.1 compatibility with MacBook Neo (A18 Pro)?
by Ronald Hamilton 22 Apr '26

22 Apr '26

Hi ChimeraX team, I'm considering running ChimeraX 1.11.1 on the new MacBook Neo (A18 Pro, 2026). I noticed the Apple Silicon build is listed as M-series only, so I assume the universal build would be the right one to use. Has the team had a chance to test ChimeraX on the MacBook Neo? Are there any known issues I should be aware of? Thanks for your time and for the continued development of ChimeraX! Best regards, Ronald Sent from Outlook<http://aka.ms/weboutlook>

4 3

Re: ChimeraX locks up in a Mac
by Tom Goddard 22 Apr '26

22 Apr '26

Hi Joseph, This ChimeraX error on Mac is caused by a bug in the Qt window toolkit which appeared with macOS 26. The current ChimeraX daily build uses a newer Qt version (6.10) which appears to fix the problem. The daily build is quite stable, so you may want to use it. It is on the ChimeraX download page. Thanks for the info about Report Bug not working once you hit this error. It must work for some people because this ChimeraX error has been reported dozens of times. Tom > On Apr 21, 2026, at 8:15 PM, Beckman, Joseph S <joe.beckman(a)oregonstate.edu> wrote: > > I wanted to report a reoccurring problem I have been having for the past two months. > > While the program is sitting open and unused, this message popped up and I have to close the program from the kill panel (opt-Escape) > > > > > > I have tried to use Report Bug, but the pop up window does not allow me to edit anything. The machine and software ID show in the window are correct. > > Thanks for all the support you provide, I learn a lot from the posts but am just an amateur. > > >

1 0

how to hide all for a specified spec
by Daniel David Richman 22 Apr '26

22 Apr '26

Hi users, Often when I open a PDB, some residues are shown in both cartoon and atomic display. Often I want to hide both displays, and I can’t figure out how to do this. For instance open 7ubj hide #1 // hides only the atoms hide #1 all // gives an error hide #1 cartoons // this seems to be the only way to hide the cartoons? same story with, for instance hide #1/A Am I missing something? I’m running 1.11.1 on Mac. Thanks, Daniel

4 4

Re: Boltz pae contacts
by Tom Goddard 21 Apr '26

21 Apr '26

Hi Nathan, The error message "No alphafold specified for alphafold contacts" is goofed up -- it should say "No atoms specified for alphafold contacts". This means your structure has no chain A, so your command "alphafold contacts /A to /B distance 5 maxpae 6" needs to be modified to use the actual chain identifiers in your structure. You can hover the mouse over the chains in your structure and it will popup some text indicating the chain id under the mouse. Yes the "Alphafold Error Plot" in ChimeraX works for Boltz 1 and 2, AlphaFold 2 and 3, OpenFold 3, and ESMFold predictions. I plan to rename it Predicted Aligned Error Plot so it will be clearer that it is not specific to AlphaFold. It currently has the AlphaFold name because when I added AlphaFold 2 support about 4 years ago there were no other prediction programs writing PAE. I have fixed the text of the error message in the daily build. Thanks for reporting the problem. Tom > On Apr 21, 2026, at 4:41 PM, Nathan Davis <ndavis18(a)uwyo.edu> wrote: > > I get the error: No alphafold specified for alphafold contacts. I attached my chimerax session. Should I be using alphafold error plot for the pae? > > On Apr 21, 2026, at 11:06 AM, Nathan Davis via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: > > Hi, I'm Nathan. I have been using ChimeraX to assess protein-protein interfaces. One of the commands I use is alphafold contacts, usually with something like this: alphafold contacts /A to /B distance 5 maxpae 6. I started looking at boltz runs as well and realized that this command does not work for boltz models. Is there a similar command that would work for boltz? Also, I'm importing boltz models that I ran on my local cluster. > > Thank you! > Nathan

1 0

Boltz pae contacts
by Nathan Davis 21 Apr '26

21 Apr '26

Hi, I'm Nathan. I have been using ChimeraX to assess protein-protein interfaces. One of the commands I use is alphafold contacts, usually with something like this: alphafold contacts /A to /B distance 5 maxpae 6. I started looking at boltz runs as well and realized that this command does not work for boltz models. Is there a similar command that would work for boltz? Also, I'm importing boltz models that I ran on my local cluster. Thank you! Nathan

2 1

Sequence selection and export tools
by Samuel Haysom 21 Apr '26

21 Apr '26

Hi, Not sure if I'm missing this but there are a few sequence selection and export tools that I can't seem to find an easy way to do: 1. Is there a way to select two locations on a protein chain and then expand the selection to include all the residues between those two points? 2. If a continuous stretch of residues is selected, is there a way to print the sequence to the log or to copy it to the clipboard? 3. In the sequence view, is there a way to select a stretch of residues and then copy that to the clipboard? In general it would be really nice if copy worked in the sequence view window on selected residues I'm aware that I could script this functionality but it does seem to the sort of thing that might be possible in the vanilla installation. KR, Sam Samuel Haysom Senior Scientist • Protein Sciences Nxera Pharma +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. Nxera Pharma UK Limited. Registered Office: Granta Park, Great Abington, Cambridge, Cambridgeshire, CB21 6DG. Company No: 06267989

3 2

Chimera X color question
by Michael Moos 14 Apr '26

14 Apr '26

Hello, I try to color different parts of a molecular chain and am stuck with the problem that I can not define the fill color individually for the selected parts. The color is valid for the selected sticks but fill color changes for the whole molecule. Is there a solution for this problem? It works if I cut the molecule in different parts but I would like to keep it as whole. The program itself is very nice and I prefer to use it for displaying long molecules. A color code would be necessary for marking the different parts of the molecule for better visualization (see attached file). Kind regards, Michael -- Dipl. Chem. Michael Moos Universität Würzburg Institut für Organische Chemie Lehrstuhl für Physikalische Organische Chemie AK Prof. Lambert Am Hubland C1 97074 Würzburg Phone: +49931 31 88764 Fax: +49931 31 88764-0 Web: https://www.chemie.uni-wuerzburg.de/oc/lambert-group/

2 4

Re: [Chimera-users] Built-in residue specific annotations in mmCIF?
by Oliver Clarke 13 Apr '26

13 Apr '26

Hi all, Bringing back a long-forgotten thread from the dead... Would it be possible to incorporate self-contained annotations into mmCIF in ChimeraX (reading/writing)? I recently added a primitive little widget to do this in coot1-trimmings: https://bsky.app/profile/olibclarke.bsky.social/post/3micblpuoxc2u This adds the notes as base64 in a loop at the end, so they are persistent and can be read/written/modified by multiple users, with timestamps & 3D coordinates for each note: _cootnote_annotation_meta.version 1 _cootnote_annotation_meta.program coot-trimmings loop_ _cootnote_residue_note.id _cootnote_residue_note.auth_asym_id _cootnote_residue_note.auth_seq_id _cootnote_residue_note.pdbx_PDB_ins_code _cootnote_residue_note.label_comp_id _cootnote_residue_note.author_b64 _cootnote_residue_note.modified_utc _cootnote_residue_note.note_b64 1 A 162 ? GLY T2xp 2026-03-31T17:06:58Z dGhpcyBnbHljaW5lIGlzIHdlaXJk 2 A 196 ? GLU T2xp 2026-03-31T17:07:41Z 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 3 C 3006 ? K T2xp 2026-03-31T17:08:08Z VGhpcyBpcyBvbmUgb2YgdGhlIHBvdGFzc2l1bXM= The nice thing about this is it is very flexible, and it means the structure itself can contain a record of modifications, interesting sites, disease mutations, etc - and can also become a kind of "track changes" or discussion forum for the structure - facilitating conversations between collaborators, for example. If there is interest, it might be good to identify a shared format for such a loop, so notes written in Coot could be read/navigated in ChimeraX, & vice versa? Cheers Oli > On Nov 12, 2015, at 7:08 PM, Greg Couch <gregc(a)cgl.ucsf.edu> wrote: > > Noted. I've added this to the list of things to do for ChimeraX (formerly known as Chimera2). > > -- Greg > > On 11/12/2015 02:21 PM, Oliver Clarke wrote: >> Relating to this, I wonder whether it is possible to find a home for attributes calculated in Chimera 2 in one of the mmCIF fields? >> >> I mean that's the advantage of mmCIF in theory right, that it is extensible and can support attributes beyond just position and B-factor? >> >> This would make transferring custom defined or calculated attributes between different chimera sessions much easier I think, if they were inherent to the file containing the coordinates, and again would at least allow for the possibility of data exchange with other programs. >> >> Oliver. >> >> On Thu, Nov 12, 2015 at 4:49 PM, Oliver Clarke <olibclarke(a)gmail.com <mailto:olibclarke@gmail.com>> wrote: >>> I see what you mean Greg... it is not at all clear how to use this now that I look at it in more detail. >>> >>> A hack using this entry as a handle for persistent notes would certainly be useful in the medium term, but in the longer term it would be nice to have a established syntax, so that notes written in Chimera could be read and displayed in Coot, for example (see here for discussion: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=coot;8213db52.1511) >>> >>> But I guess this might require some discussion with the PDB - according to their FAQ old-school PDB files will become obsolete next year and mmCIF/PDBx will be the only game in town... >>> >>> Cheers, >>> Oliver. >>> >>> On Thu, Nov 12, 2015 at 4:22 PM, Greg Couch < <mailto:gregc@cgl.ucsf.edu>gregc(a)cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>> wrote: >>>> That is an excellent suggestion. Currently the mmCIF files from the PDB provide the free-form text for the footnote, but do not provide the data that is supposed to be in the associated conformer_family_coord_set category. And without that data, it will be difficult to figure out and show exactly which atoms/residues are associated with the footnote. It looks like that part of the mmCIF specification is unused because it is not well thought out. The conformer_family_coord_set data category makes references to CIF save frames, but currently " mmCIF does not support references to save frames or the use of save frames for purposes other than for encapsulating dictionary definitions" [ <http://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html>http://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html] And since there are no examples, so it is unclear how the mmCIF committee was expecting this to work. >>>> >>>> So until atom_sites_footnote's are "fixed", is getting access to the text okay? We could probably extract the relevant residues from the free-form text most of the time, but it would be a hack. >>>> >>>> -- Greg >>>> >>>> >>>> On 11/11/2015 10:11 AM, Oliver Clarke wrote: >>>>> Hi all, >>>>> >>>>> As discussed on the ccp4bb ( <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511>https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511) the mmCIF format incorporates an atom_sites_foornote record ( <http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_site…>http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_site…) which allows for the direct association of specific comments/annotations with particular atoms/residues. >>>>> >>>>> As part of expanding mmCIF support in Chimera2, would it be possible to consider incorporating the capacity to read, write, and display these records as labels or notes? This could be a great way of incorporating built-in-annotations in a structure pertaining to specific features that could potentially be readable by other software such as Coot and pymol. >>>>> >>>>> Cheers, >>>>> Oliver. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Chimera-users mailing list >>>>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> >

3 7

Help with command-line orientation of structure in ChimeraX
by Nusrat Tazkia 13 Apr '26

13 Apr '26

Dear ChimeraX Support Team, I hope you are doing well. I am currently working with spike protein structures in ChimeraX and would like to orient them in a consistent and reproducible way using command-line instructions. Specifically, I am trying to “straighten” the structure so that the receptor-binding domain (RBD) is oriented upwards, without relying on manual mouse adjustments. The RBD in my structure corresponds to residues 319–541 (chains A, B and C). I have been using commands such as 'measure inertia', 'view', and 'turn', but I am having difficulty determining the exact sequence needed to achieve a clean and consistent orientation. I have attached a .cxs session file showing my current structure and preferred manual orientation. I actually have many similar .cxs files, so I am looking for a command-line approach that will reliably produce the same orientation across all of them. Additionally, when I use 'movie encode' to generate a rotation, I notice that the structure slightly tilts to the left or right during rotation. I would like the structure to remain perfectly straight and spin cleanly along a single axis (ideally the y-axis), without any unintended tilt. Would it be possible for you to suggest the appropriate commands (or workflow) to reproduce this view consistently and achieve a stable, axis-aligned rotation? Thank you very much for your time and support. Kind regards, Nusrat Tazkia

3 6

Orbital Viewer - Gaussian formatted checkpoint
by Matthias Bremer 08 Apr '26

08 Apr '26

Dear All, when trying to render molecular orbitals from a Gaussian .fchk file, I get the following error message: WARNING AaronTools.fileIO.FileReader.read_fchk could not create Orbitals, try increasing the max. array size to read from FCHK files I used the 6-31+G(d) basis. How can I fix this? Best regards Matthias Bremer

2 1

vseries movie recording with frame labels
by Rayees Mattoo 06 Apr '26

06 Apr '26

Hi, I want to record a vseries movie, a total of 20 frames (frame 0-19). I used the below script. I want to include a frame label (Frame 0 to 19) as the movie oscillates across frames. The frame numbers should appear in sync with the movie frames. How can I include that and record with vseries? movie record; vseries play #1 direction oscillate loop true; wait 200; movie encode ~/Desktop/vseries_movie1.mp4 Best Rayees

2 2

Visualizing contact sites on structures larger than atoms
by Wilson, Melissa (NIH/NINDS) [F] 03 Apr '26

03 Apr '26

Hello, I am currently using ChimeraX to reconstruct mitochondria undergoing autophagy. I am interested in visualizing contact sites between the mitolysosome, surrounding mitochondria, and endoplasmic reticulum. The clashes/contacts command<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/clashes.html#options> is all in the context of atoms. Can this command be used for the purpose of larger structures? Or is there another method in ChimeraX to achieve such a visualization? All of my models are surfaces. Best, Melissa Wilson

2 1

Issue with SVG export in CircosContacts plugin: Interface residues missing !
by Arun Gupta 03 Apr '26

03 Apr '26

Dear ChimeraX Team, Today I tested the CircosContacts plugin in ChimeraX to generate Circos plots for the peptide–MHC interface. The plugin works as expected in the CircosContacts HTML webpage, where I can see the interface residue/atom contact details between the peptide (Chain Id - C) and MHC chain (Chain Id- A). However, I am not able to observe the interface residues in the exported contacts_circos.svg file. The SVG export appears to be missing the interface residue annotations that are visible in the HTML view. I have attached the exported contacts_circos.svg file for reference. For reproducibility, I used the following command: circoscontacts #1/A restrict #1/C outputDir /Users/arungupta/010426_contacts_1 interModel true intramol false Could you please let me know whether this is expected behavior, or if there is a workaround to ensure that the interface residues are included in the exported SVG file as well or if this is a known limitation of the current version of the plugin ? Thank you for your time and for developing such a useful plugin. Best regards, Arun Arun Gupta PhD, MRSC Sr. Post Doctoral Research Assistant Gillespie/McMichael Group Nuffield Dept. of Clinical Medicine, University of Oxford, Centre for Immuno-Oncology Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ

4 4

OpenFold Tool Model Selection Question
by Eidman, Zachary M 02 Apr '26

02 Apr '26

Hello, I’ve recently started using the OpenFold tool in ChimeraX and I’ve found it really useful so far. I’m trying to model multimeric complexes and I’m wondering if the tool automatically detects multimeric inputs and uses OpenFold Multimer as the model? I noticed in some config files there is code that detects monomeric versus multimeric input, but I don’t see any indication of what model is used in any of my output files. Any input would be greatly appreciated. Thanks! Zach Eidman

3 4

Boltz Error in ChimeraX on Ubuntu 24 LTS (GPU Workstation)
by Neha Gandhi 02 Apr '26

02 Apr '26

Dear Team, I hope you are doing well. I am writing to report an issue with running Boltz within ChimeraX on my Ubuntu 24 LTS GPU workstation. Until yesterday, Boltz was functioning correctly and I was able to successfully predict protein–ligand binding affinities. However, starting today, the workflow has begun failing with an error (line 125) during execution. I have tried the following troubleshooting steps: - Reinstalled ChimeraX and tested both the daily build and version 1.12 - Verified GPU functionality (other tools such as OpenFold are running without issues) Current behavior: - Boltz successfully predicts ligand-only structures - Boltz successfully predicts protein-only structures - However, it fails when attempting protein–ligand complex predictions. I tried using command line but didn't work. This suggests the issue may be specific to the combined workflow rather than general installation or GPU configuration. Could you please advise on: 1. Possible causes for this error (especially related to recent updates or dependencies)? 2. Any logs or debug steps I should provide? 3. Recommended fixes or configuration changes? I would be happy to share error logs or system details if needed. Thank you for your support. Best regards, Neha Gandhi Get Outlook for Android<https://aka.ms/AAb9ysg>

2 2

addh to only parts of a model?
by Alexis Rohou 01 Apr '26

01 Apr '26

Hi all, As specified in the documentation, in command addh, "Hydrogens are added to entire atomic model(s) even if only parts of models are specified." Given how specifically this is stated, I'm guessing there was a good rationale for doing it this way. However I am facing a situation where I'd really, really like to add hydrogens only to waters (which were added by Servalcat). For reasons that I haven't got to the bottom of, addh adds hydrogens in the wrong places in a ligand I'm working on (a peptide with a mixture of natural and non-canonical amino acids, though I'm almost certain I've observed this behavior with other, less exotic, ligands). So: what is/was the rationale for not allowing users to add hydrogens to only parts of a model? How would the developers feel about a pull request adding an option to override this behavior and only add hydrogens to the spec supplied by the user? Cheers, Alexis

2 1

Question about multiple sequence alignment after structural superimposition in ChimeraX
by OLIVA MIGUEL, BALDOMERO 31 Mar '26

31 Mar '26

Dear ChimeraX Team and Community, First, I would like to apologize if my question is redundant. I have only recently joined the community and may have missed previous discussions on this topic. I have been a user of Chimera on macOS, but with the most recent macOS updates, I have encountered compatibility issues that have led me to transition to ChimeraX. I am currently adapting to the new interface and commands, and I appreciate the many improvements it offers. However, I am missing a feature that I frequently used in Chimera: the ability to obtain a multiple sequence alignment after superimposing several structures using MatchMaker. This functionality was very useful in my workflow. I would like to ask whether there is an alternative approach in ChimeraX to achieve this, or if there are plans to include similar functionality in future updates. Thank you very much for your time and assistance. Baldo Oliva -- -- --------------------------- e-mail:baldo.oliva@ <e-mail%3Abaldo.oliva(a)gmail.com>upf.edu Baldo Oliva Miguel, PhD Structural Bioinformatics Laboratory (GRIB-IMIM) Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine (PRBB) C/ Doctor Aiguader, 80. Barcelona-08003, Catalonia, Spain (EU) Tfn: 34-933160509 Fax: 34-933160550

2 1

color the inside of ribbon helix differently
by Daniel Larsson 30 Mar '26

30 Mar '26

Hi ChimeraX team, I would like to color the inside of alpha helices in a different color from the outside, which is a standard feature in PyMOL and the original Chimera program: https://pymolwiki.org/Cartoon_highlight_color https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribinsidecolor.html But my understanding is that this is not currently possible in ChimeraX. I found some old mailing list threads on the topic and this 5-year-old open feature request ticket with priority set to low: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu… https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/1719 Based on comments from the developers, it seems as if implementing this feature is not very straight-forward with the current ribbon rendering engine. Still, I hope you will elevate the priority and put it on the road-map for future releases as it greatly improves visibility and 3D-feeling of large ribbon-style protein structures. It would add another important tool for users of your excellent software. Best regards, Daniel 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 1

ChopChopMF — official user guide now available
by Lukas Bauer 30 Mar '26

30 Mar '26

Dear ChimeraX community, An official user guide for ChopChopMF is now available. ChopChopMF is a ChimeraX plugin designed to streamline protein structure analysis — providing a GUI-based workflow for mapping sequence alignments, mutations, and protein-protein interfaces directly onto 3D structures, without requiring extensive command-line expertise. The user guide covers installation, usage, and practical workflows: https://lukasinscience.github.io/ChopChopMF/ The plugin can be installed directly from the ChimeraX Toolshed: https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxchopchopmf Feedback and suggestions are very welcome. Best regards, Lukas

1 0

Question about clipping and transparency
by John Watters 30 Mar '26

30 Mar '26

Hello All, I am experiencing an issue when I am trying to make a movie of a series of coupled atomic models and volumes overlaid on top of each other. I cannot seem to make what I believe is called the "surface cap" transparent when I have clipped into a volume and I am showing/changing the volume. When I call the transparency command in ChimeraX itself (without the script running) it works as it should and makes the surface cap transparent, but in the movie-making script it seems like the transparency command is having no effect? Do you have any suggestions on how to deal with this? Thank you! Example .cxc code block attempt clip off; clip near -24.984; transparency #1.1 90; ######################### hide #!*.*; hide #!* models; show #!1.2 models; #show volume show #!3 models; #show atomic model transparency #1.2 90;transparency #1.2.1.1 90; wait 3 hide #!*.*; hide #!* models; show #!1.3 models; show #!4 models; transparency #1.3 90;transparency #1.3.1.1 90; wait 3 ######################### Best, John

2 1

How to generate an alignment to color by conservation
by Victor Ruiz-Arroyo 25 Mar '26

25 Mar '26

Dear ChimeraX staff, I am trying to make a representation to display the conservation using a color scale similar to this tutorial: https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-… I have downloaded ~500 target proteins using blast, downloaded the results, and aligned them in clusta omega, which gave me this file: [image: image.png] However everytime I try to open it in chimeraX I get this matrix-like window: [image: image.png] Which is different to what I would expect based on the tutorial. In fact, if I download the .ali from the tutorial, I see the correct alignment window. I have tried different alignment formats without success, and I still get the "matrix window". What software and format do you recommend using in Chimerax? Best Victor

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chimerax-trimmings update
by Oliver Clarke 25 Mar '26

25 Mar '26

Hi all, For anyone using chimerax-trimmings, I gave it a bit of an update: https://github.com/olibclarke/chimerax-trimmings/ I reorganized it and cleaned it up, added more documentation, and took advantage of the new "synopsis" option for aliases to add a help strinng for each alias, so you can access usage info from the command line (typing help or usage followed by the alias name). I also added function keys to toggle shown models on and off, and to toggle shown maps on and off, as well as function keys to cycle through lighting presets, and a function key to cycle through model display options. Hope they are useful to some folks, let me know if so! Cheers Oli

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