- ChimeraX-users - RBVI Mailing Lists

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

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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):

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Publication Request
by Russell Couch 29 Aug '25

29 Aug '25

Hello UCSF! My name is Russell and I am a 17 year old student seeking approval from the developers to use ChimeraX in the publication of educationally-intended (not commercially-intended) content I would like to design using the program and animate separately. I would like to use ChimeraX to, for example, compile individual proteins into a complete infectious pathogen in order to demonstrate the roles of individual proteins in the process of infection, disease progression, and possible treatment. I want to firmly state that my personal purpose of the publication is educational, though I understand YouTube is inherently a commercial platform. When complete, the videos would be uploaded to a brand new, unmonetized channel dedicated to my educational publications. There would be no other co-collaborators, as in people frequently working with me and using ChimeraX to produce educational content. This is a personal project and I would be the only one using the program to produce my content. If another creator wanted to collaborate with me using their own research and resources (assuming they have all the proper permission like I'm asking for), would that be allowed, assuming the collaboration is occasional and on a per-video basis rather than consistent or unifying, such as two channels deciding to join together? On a bit of a more personal note, I am applying to college soon and am very interested in a couple of colleges in California. I am very passionate about engineering, particularly chemical engineering, and I believe the cures of tomorrow are waiting to be discovered. I am on a mission to discover them and make them available to all. While I am determined to be the change I want to be no matter where I go, I would like to attend a good engineering school if possible, and am personally very attracted to the idea of going to college in California. Some of the very best engineering schools in the country are in California, and getting into them would be a dream come true, though I am realistic and prepared to achieve my goals without any of their external resources. These resources, while valuable, mean nothing without the internal drive to strive. Regardless of acceptance, the colleges in California most intriguing to me are UCB, Caltech, and Stanford, though UCSD, Irvine, Davis, and many other schools there all have fantastic engineering programs, and are more statistically favorable in terms of acceptance, though still quite selective. I know UCSF is a medical school, but it shares with these colleges very high selectivity, and I would love to gather any potential advice, especially coming directly from another top college. I greatly appreciate you taking the time to read my request and am very excited to use ChimeraX, whether for personal or educational use. Sincerely, Russell Couch

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Coloring different regions
by Vojo P Deretic 29 Aug '25

29 Aug '25

Hi How to color different domains in a structure in ChineraX. I tried selecting residues on the sequence and can get an outline over the selection but how do I color different regions and keep all of them differently colored plus save the work? Thanks Sent from my iPhone with lots of typos and autocorrect nonsense - my apologies...

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ISOLDE installation error
by Zhou, Tongqing (NIH/VRC) [E] 27 Aug '25

27 Aug '25

Dear All, I am having problem install ISOLDE on a new MacBook. My ChimeraX version is 1.10rc202505310246 (2025-05-31). When installing from Toolshed, it says: ERROR: Could not find a version that satisfies the requirement ChimeraX-Core~=1.10.0 (from chimerax-isolde) (from versions: none) ERROR: No matching distribution found for ChimeraX-Core~=1.10.0 Best regards, Tongqing Tongqing Zhou, Ph.D. Principal Investigator and Chief Structural Virology and Vaccinology Section Structural Biology and Structural Bioinformatics Cores Vaccine Research Center (VRC), NIAID National Institutes of Health Building T40, Room 117 (Office) Building 40, Room 4609B (Lab, shipping) 40 Convent Drive, Bethesda, MD 20892 Office: (301) 761-7068 Cell: (240) 695-0536 https://www.niaid.nih.gov/research/tongqing-zhou-phd tzhou(a)nih.gov<mailto:tzhou@nih.gov>

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Displaying maps with threshold defined by mapstats
by Grundmann,Lorenz Emanuel 27 Aug '25

27 Aug '25

Dear ChimeraX-Team and all, I want to visualize multiple cryoEM maps in a comparative manner. Therefore, I would like to display them with a threshold level of e.g. 90% their maximum voxel value. Is this possible in chimerax? Any help would be greatly appreciated. Thank you. Best, Lorenz

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aborting slow hbonds command
by Daniel Larsson 25 Aug '25

25 Aug '25

Is it possible to prematurely stop a command issued on the command line that takes too long time? I often have sessions with many (more than 20) large ribosome structures open at the same time. I sometimes mistype the restrict atom-spec2 argument for the hbonds command and ChimeraX goes through each of the structures one by one twice, which can take very long time. I wish there were a flag to the hbonds command to only consider the models in atom-spec1, so that those typos does not spawn a search across all models. In addition, it would be great if the code for the hbonds command could be optimized. Why iterate over all models if only atoms in one model are in atom-spec1? 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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ISOLDE released for ChimeraX 1.10
by Tristan Croll 22 Aug '25

22 Aug '25

Hi all, Just a note for ISOLDE users: ISOLDE 1.10 is now out on the TooShed, ready for use with ChimeraX 1.10.x. Please enjoy! Best, Tristan -- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT

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Model-Map coloring using the ChimeraX
by Andrew Mugo 21 Aug '25

21 Aug '25

Dear ChimeraX user support team, I am having a problem of coloring map based on the model color. I uninstalled and re-installed ChimeraX 1.9/1.10 but when I try to color the map, the software gives electrostatic color like. Please let me know how I can solve this problem. Best regards, Andrew

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Residue Interaction Network visualisation using chimerax
by Gagandeep Singh 20 Aug '25

20 Aug '25

Dear team , I have generated residue interaction network (RIN) data using RING 4.0 and would like to visualize this . I am familiar with UCSF Chimera, which supports visualization of RIN data, and I was wondering if ChimeraX also offers similar functionality. Kind regards -- *गगनदीप सिंह **/ Gagandeep Singh* *डॉक्टरेट का विद्यार्थी **/ Doctoral student* *ब्रिक - ट्रासलेशनल स्वास्थ्य विज्ञान और प्रौद्योगिकी संस्थान* *BRIC- Translational Health Science and Technology Institute* *(भारत सरकार के जैव-प्रौद्योगिकी विभाग का एक स्वायत्त संस्थान)* *(An autonomous institute of the Dept of Biotechnology, Govt Of India)* *NCR Biotech Science Cluster,* *3rd Milestone, Faridabad–Gurugram Expressway,* *PO box #04, Faridabad- 121001 (Haryana)*

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