December 2025 - ChimeraX-users - RBVI Mailing Lists

NEED HELP TO INSTALL BOLTZ2 in CHIMERAX.
by Dr. V.N. Balaji 07 Dec '25

07 Dec '25

Subject: Bug Report: "Intel Mac" Error Blocking Boltz Install on Windows 11 (NVIDIA 3080 Ti) Dear ChimeraX Team, I am writing to report a platform detection bug in the Boltz installer within ChimeraX (Daily Build 1.12.dev202512040236). When attempting to install Boltz via the boltz install command on a Windows 11 system with a compatible NVIDIA GPU, the installation fails immediately with the following error: "Boltz requires newer Torch versions that are not available on Intel Macs." This appears to be a false positive in the installer's logic, erroneously flagging my Windows/x86_64 system as an unsupported Intel Mac. System Configuration: OS: Windows 11 Pro (x86_64) CPU: Intel Core i9-7940X GPU: NVIDIA GeForce RTX 3080 Ti (12GB VRAM, CUDA 12.x active) ChimeraX Version: 1.12.dev202512040236 (2025-12-04) Context & Troubleshooting: Verified Hardware: I have already successfully installed and verified boltz (v2.2.1) in a standalone PowerShell environment on this same machine; it runs protein-ligand docking with GPU acceleration without issue. Workarounds Attempted: I have tried running ChimeraX in admin mode, using different daily builds, and attempting to manually intervene with pip, but the internal installer aborts before package retrieval begins due to this platform check. Request: Could you advise on a command-line flag or manual workaround to bypass this platform check and force a Windows/CUDA installation? Alternatively, if this requires a patch to the installer script to correctly identify Windows environments, please let me know. Thank you for your assistance. Best regards, V.N. Balaji, Ph.D. Computational Chemist Bangalore, India vnbalaji(a)gmail.com | LinkedIn: vnbalaji

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Can ISOLDE-refined models be directly deposited to the PDB?
by man6ny＠virginia.edu 05 Dec '25

05 Dec '25

Dear all, Maybe an ignorant or previously-asked question... I believe most people refine cryo-EM models using e.g. Phenix real-space-refine before depositing them to the PDB. Is there a strict reason (practical or philosophical) why cryo-EM models refined in ISOLDE cannot be directly deposited without subsequent refinement in Phenix or Refmac? I have a high-resolution map (2.2 A) but the latter programs seem to actually make my model worse (e.g. Phenix tends to give me rotamers that are not supported by the experimental data). I would prefer to use the model refined in ISOLDE but perhaps I am missing something? Many thanks for your insight! Louis

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Opening multiple chimeraX windows at the same time?
by Choy, Jon 05 Dec '25

05 Dec '25

Hi Oliver and Tom or whom it may concern, I was interested in whether it is possible to open multiple .cxs files at the same time? I am comparing structural features across many different proteins and their corresponding maps—and it is very annoying to be only able to open one map and its protein at a time. Although it is possible to load multiple resolved structures and their maps into a single .cxs file, these structures all load onto different spots on the chimeraX interactive space—making side by side comparison a bit cumbersome. Assistance in this would be massively appreciated! Thank you so much and looking forward to hearing from you. Best, Jon

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Calcium ions labeled as solvent, not as ions
by Ute Roehrig 05 Dec '25

05 Dec '25

Hello, I am not sure if this is a problem in the structure or in ChimeraX or intentional, but I remarked that in PDB structure 7tba the calcium ions are labeled as "solvent" and not as "ions", although the element and atom type seem to be OK. I did not see the same in other PDB structures with calcium. Thank you for your help, Ute

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Subject: Request for Detailed Clarification on ChimeraX RMSD, Alignment Metrics, and Pruning Calculations
by EMMANUEL JAIME SIBAYAN 05 Dec '25

05 Dec '25

Hello, Good day. I am using ChimeraX for an academic research project involving protein structure comparison. Before proceeding with my analysis, I would like to request detailed clarification on how ChimeraX obtains specific structural comparison values. In particular, I would like to understand: how ChimeraX gets these values and what formulas or computational methods are used for each measurement. Specifically, I would like to ask about the following: 1. The recommended procedure for computing RMSD between two protein structures in ChimeraX, including the appropriate steps, commands, and settings to ensure a correct and reproducible measurement. 2. How ChimeraX determines aligned residue pairs during Matchmaker or similar alignment tools, including how residues are selected or excluded based on sequence alignment and structural fit. 3. The exact meaning and calculation method for “pruned atom pairs” in the alignment results. In particular, I would like clarification on the pruning process (for example, removal of atom pairs whose distances exceed a threshold) and how this affects the final reported values. 4. Whether RMSD in ChimeraX is calculated using all aligned atom pairs, pruned atom pairs only, or whether both values are available. I would also like to understand how to correctly interpret RMSD before pruning versus RMSD after pruning. 5. How ChimeraX performs structural alignment when the two sequences are identical but the predicted models have local deviations such as altered loops, turns, flexible regions, or insertions. 6. Recommended best practices when comparing three types of structures: • an experimental PDB crystal structure • an AlphaFold predicted structure • a Swiss-Model homology model 7. Any documentation, reference materials, or example workflows that explain the statistical reporting of structural comparison in ChimeraX, especially the following values: • RMSD, calculated as √(1/N Σ di²) • distance measurements between paired atoms, defined as √[(x1 − x2)² + (y1 − y2)² + (z1 − z2)²] • aligned residue counts • pruning thresholds and post-pruning atom pair counts This information will help ensure that the statistical evaluation in my study (including RMSD, aligned residues, and pruned atom pairs) is methodologically correct and consistent with ChimeraX standards. Thank you very much for your time and assistance. Your guidance will greatly improve the accuracy and reliability of my research analysis. Best regards, [Your Name] -- *The information or attachment(s) in this email is(are) strictly confidential and is(are) for the intended recipient only. Any unauthorized use, dissemination, or copy of this message or the information it contains is prohibited. The recipient has the responsibility to ensure the protection of any personal data included in this e-mail and its attachment(s). If you are not the intended recipient or you receive this email by mistake, please notify the sender immediately and delete the original message and attachment(s).*

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Recording High Quality MD Trajectory Movie in ChimeraX
by Gourav Das 03 Dec '25

03 Dec '25

Dear ChimeraX users, I am recording the MD trajectory of a simulation as a movie in ChimeraX. However, the output quality of the movie is very low. How can I improve the quality of the movie? I would appreciate your guidance regarding this issue. Thank you for your support. With regards, Gourav Das Research Scholar Indian Institute of Technology Kharagpur West Bengal, India-721302 Mob: +91-6295251060 --

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RHEL/Rocky/AlmaLinux/etc 10 releases available
by Greg Couch 03 Dec '25

03 Dec '25

We are pleased to announce that you can now get 1.11 release candidates and daily builds for Red Hat Enterprise Linux 10 and derivatives. For example, Rocky 10 and AlmaLinux 10. A more complete list can be found on wikipedia, https://en.wikipedia.org/wiki/Red_Hat_Enterprise_Linux_derivatives. Since this is a new platform for ChimeraX, it hasn't been tested as thoroughly as the other platforms. We expect the RHEL 10 releases to be bug-for-bug compatible with the RHEL 9 releases, but there is a chance that they aren't. So please try one out and report any bugs you find. -- Greg

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Colouring Amino Acids Within A Selected Region
by Nusrat Tazkia 03 Dec '25

03 Dec '25

Hello ChimeraX developpers, I hope you are doing well. I was trying to colour each amino acid present within a selected region of my model and couldn't figure out how to do it. Could you please guide me on how to do it? I ran these commands (for examples for chains A and E) and have attached my model in this email as well: interfaces select /A contacting /E bothSides true color sel red Please let me know at your earliest convenience. Thank you, Nusrat Tazkia

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How to measure the correlation length of a map in ChimeraX
by 张楠 02 Dec '25

02 Dec '25

Dear ChimeraX Developers, I have an EM density map and need to measure its diameter and height. I used the "measure and color blob" tool, which displays the length, width, and height of the entire EM density when clicked. However, the values are measured around the entire density map, making them slightly larger than the actual diameter. Therefore, I tried using the "tape" tool to measure, but it is difficult to select two perfectly horizontal points for an accurate measurement. I would like to ask how to measure the correlation length of a map in ChimeraX. Looking forward to your answer, thank you! Best regards, Nan Nan Zhang zhangnan(a)nankai.edu.cn

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Alpha-fold-chimerax-coot - incompatibility
by Abhilash Padavannil 01 Dec '25

01 Dec '25

Hi All, I am having trouble with .cif files in Chimerax — I re-built the model (Model-Angelo) in coot using alpha-fold models for completion and saved it as a .cif file. When I open the file in Chimerax certain proteins in the complex show up differently and the their chain IDs are missing in the Chimerax list. Could you help me fix this ? Previously I was able to combine the individual alpha-fold models to a single in Chimerax .cif file. However, if I do local refinement in coot the chains go back to being different. Please suggest. Attached is the screen shot for reference. Thank you. [cid:d13d01b7-12bf-4117-8bbe-f63d6679629a@namprd08.prod.outlook.com]

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