- ChimeraX-users - RBVI Mailing Lists

regional minimization?
by Daniel David Richman 12 May '26

12 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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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 01 May '26

01 May '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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