September 2025 - ChimeraX-users - RBVI Mailing Lists

ChimeraX 1.8 user manual
by NUR SYAMIM SYAHIRAH MAT HUSSIN 05 Sep '25

05 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>

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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

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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.

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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

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How to apply selected graphics JUST to the side chain and not the backbone?
by mfmccl＠berkeley.edu 03 Sep '25

03 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

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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

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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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