- ChimeraX-users - RBVI Mailing Lists

ChimeraX Boltz prediction running eternally
by Sam Allen 10 Dec '25

10 Dec '25

Hello Tom and co., I am currently trying to use ChimeraX Boltz tool to predict the structure of some small ligands onto a GPCR and my prediction running timer just never stops. I initially attempted to install and run the tool on Windows but the install failed to import the mols folder properly multiple times (uninstall and reinstalled), after manually untaring the folder in Powershell it still didn't run (Timeout while submitting to MSA server). I then decided to switch over to my mac (M1 16GB) and while the install of Boltz in ChimeraX no longer had any error and the prediction didn't error either, the timer just continued to go up (to 26000 eventually). I figured the protein was too large (471 residues, makes sense), so I tried to rerun one of your test examples (8rf4, https://www.rbvi.ucsf.edu/chimerax/data/boltz-apr2025/runtimes.html) and still no prediction output after 20 minutes. I've tried switching from default compute device to GPU or CPU and still no difference. Additionally, in activity monitor it shows ChimeraX is taking up nearly no GPU or CPU usage, so I'm confused as to what is happening. Do you have any advice or know anything that might be going wrong that I can fix? Regards, Sam

2 1

ChimeraX Boltz prediction running eternally or failing submission to MSA server
by Sam Allen 10 Dec '25

10 Dec '25

Hello, I am currently trying to use ChimeraX Boltz tool to predict the structure of some small ligands onto a GPCR and my prediction running timer just never stops. I initially attempted to install and run the tool on Windows but the install failed to import the mols folder properly multiple times (uninstall and reinstalled), after manually untaring the folder in Powershell it still didn’t run (Timeout while submitting to MSA server). I then decided to switch over to my mac (M1 16GB) and while the install of Boltz in ChimeraX no longer had any error and the prediction didn’t error either, the timer just continued to go up (to 26000 eventually). I figured the protein was too large (471 residues, makes sense), so I tried to rerun one of your test examples (8rf4, https://www.rbvi.ucsf.edu/chimerax/data/boltz-apr2025/runtimes.html) and still no prediction output after 20 minutes. I’ve tried switching from default compute device to GPU or CPU and still no difference. Additionally, in activity monitor it shows ChimeraX is taking up nearly no GPU or CPU usage, so I’m confused as to what is happening. Do you have any advice or know anything that might be going wrong that I can fix? Update: After this email I downloaded the daily ChimeraX version and attempted to run Boltz through that. Instead now the same error as the windows appeared (No authentication provided for MSA server; Failed to process; Skipping. Error: Too many failed attempts for the MSA generation request..) Below is the error in its entirety: Running boltz prediction failed with exit code 0: command: /Users/samuelallen/boltz22/bin/boltz predict /Users/samuelallen/Desktop/boltz_testingtesting123/testingtesting123.yaml --use_msa_server --accelerator gpu --no_kernels stdout: Boltz version 2.2.0 MSA server enabled: https://api.colabfold.com MSA server authentication: no credentials provided Checking input data. Processing 1 inputs with 1 threads. Generating MSA for /Users/samuelallen/Desktop/boltz_testingtesting123/testingtesting123.yaml with 1 protein entities. Calling MSA server for target testingtesting123 with 1 sequences MSA server URL: https://api.colabfold.com MSA pairing strategy: greedy No authentication provided for MSA server Failed to process /Users/samuelallen/Desktop/boltz_testingtesting123/testingtesting123.yaml. Skipping. Error: Too many failed attempts for the MSA generation request.. stderr: 0%| | 0/1 [00:00<?, ?it/s] 0%| | 0/150 [elapsed: 00:00 remaining: ?][A SUBMIT: 0%| | 0/150 [elapsed: 00:00 remaining: ?][AError while fetching result from MSA server. Retrying... (1/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (2/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (3/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (4/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (5/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) Error while fetching result from MSA server. Retrying... (6/5) Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) SUBMIT: 0%| | 0/150 [elapsed: 01:04 remaining: ?] Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 534, in _make_request response = conn.getresponse() ^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connection.py", line 571, in getresponse httplib_response = super().getresponse() ^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1395, in getresponse response.begin() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 325, in begin version, status, reason = self._read_status() ^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 286, in _read_status line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py", line 706, in readinto return self._sock.recv_into(b) ^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1314, in recv_into return self.read(nbytes, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1166, in read return self._sslobj.read(len, buffer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TimeoutError: The read operation timed out The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/adapters.py", line 667, in send resp = conn.urlopen( ^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 841, in urlopen retries = retries.increment( ^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/util/retry.py", line 474, in increment raise reraise(type(error), error, _stacktrace) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/util/util.py", line 39, in reraise raise value File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 787, in urlopen response = self._make_request( ^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 536, in _make_request self._raise_timeout(err=e, url=url, timeout_value=read_timeout) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 367, in _raise_timeout raise ReadTimeoutError( urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/data/msa/mmseqs2.py", line 77, in submit res = requests.post( ^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/api.py", line 115, in post return request("post", url, data=data, json=json, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/api.py", line 59, in request return session.request(method=method, url=url, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/sessions.py", line 589, in request resp = self.send(prep, **send_kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/sessions.py", line 703, in send r = adapter.send(request, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/requests/adapters.py", line 713, in send raise ReadTimeout(e, request=request) requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out. (read timeout=6.02) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/main.py", line 581, in process_input compute_msa( File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/main.py", line 477, in compute_msa unpaired_msa = run_mmseqs2( ^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/data/msa/mmseqs2.py", line 201, in run_mmseqs2 out = submit(seqs_unique, mode, N) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/samuelallen/boltz22/lib/python3.11/site-packages/boltz/data/msa/mmseqs2.py", line 92, in submit raise Exception( Exception: Too many failed attempts for the MSA generation request. 100%|██████████| 1/1 [01:04<00:00, 64.69s/it] 100%|██████████| 1/1 [01:04<00:00, 64.69s/it] GPU available: True (mps), used: True TPU available: False, using: 0 TPU cores HPU available: False, using: 0 HPUs /Users/samuelallen/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 Regards, Sam

1 0

Boltz run- Kd values
by Malik, Radhika 08 Dec '25

08 Dec '25

Hello, I am a Research Scientist at Mount Sinai School of Medicine, NY. I have run Boltz in ChimeraX on a protein-ligand complex, however, I am not able to locate the file for the predicted Kd values. Can you please direct me to the file/location? I am attaching a screenshot of what I see after the run. Thanks a lot, Radhika ________________________________ Confidentiality Notice: This electronic mail transmission and any documents, files, or previous email messages attached to it may contain confidential information and are intended solely for the use of the individual or entity to which they are addressed. If you are not the intended recipient, or a person responsible for delivering such information to the intended recipient, you are hereby notified that any further review, disclosure, copying, dissemination, distribution, or use of any of the information contained in or attached to this email transmission is strictly prohibited. If you have received this message in error, please notify the sender immediately by email, discard any paper copies, and delete all electronic files of the message. Thank you for your cooperation.

4 9

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

2 2

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

4 4

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

3 2

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

3 4

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).*

2 1

bug report - pip list failure
by replacement2＠gmail.com 04 Dec '25

04 Dec '25

Hi, My apologies if this is not the best place to report a bug. There appears to be an issue with `pip list`, which may be caused by a typo in `pip.py`. Please see the traceback. It'd be great if someone can verify. Thanks. Traceback (most recent call last): File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute cmd.run(cmd_text) File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/cui5/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/pip.py", line 71, in pip pip_cmd.appendf("list") ^^^^^^^^^^^^^^^ AttributeError: 'list' object has no attribute 'appendf' cui5

4 3

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 --

2 2

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

1 0

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

2 5

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

2 1

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]

3 2

GPU/CUDA support for toolshed deep learning plugin
by HAWICKHORST, BRYAN 01 Dec '25

01 Dec '25

Hello, I am a student from Professor Jing He's lab at Old Dominion University. I am trying to enable GPU acceleration for our deep learning plugin, DeepSSETracer. The problem I am running into is that python in the chimerax environment cannot see cuda. Varying cuda versions seems to rule out including cuda as a dependency. Additionally, we would like to avoid custom cuda installations via the chimerax terminal, as it would greatly complicate installation for the users of our plugin. Is there a way to support cuda or GPU acceleration in another way (that ideally does not require user interaction with the chimerax terminal)? Or, could you point me towards tools that have managed to do this? I found this library, ONNX Runtime and wonder if it may be useful: https://onnxruntime.ai/docs/get-started/with-python.html#install-onnx-runti… Best regards, Bryan Hawickhorst Old Dominion University

2 1

Permission to create winget manifest?
by Joshua Raphael Uy 25 Nov '25

25 Nov '25

Hi Chimerax Dev team, My name is Josh Uy. I'm a graduate student at Arizona State University, and I frequently use ChimeraX as a visualization tool on both Windows and Linux! I'm wondering if you guys would be ok if I were to submit a winget <https://github.com/microsoft/winget-cli> manifest for ChimeraX? ChimeraX is a wonderful piece of software that I am using for my Ph.D and having an automated way to get and install via cli package manager tools would be incredibly handy to have. I wouldn't mind being the guy responsible for maintaining this if approved. Thank you, Josh Uy

2 1

Unable to restore session: need to install missing bundle
by GOVAERTS Cédric 25 Nov '25

25 Nov '25

Hi Team, I’m switching between computers and platforms, but now I try to reopen CXS session it fails and I get To restore session: install Animations bundle version 1.0 or newer Unable to restore session: need to install missing bundle I’ve tried the very last version of chimeraX (daily built). How can I solve this ? Thanks a bunch Cedric Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77<tel:+3226505377> Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

2 5

command history pulldown very short
by Alan Cheung 25 Nov '25

25 Nov '25

Hi There - i’m using chimerax on mac. Whenever i try to view my command history, either by tapping the up cursor or using the pop-out window, i can only ever recall 16 previous commands despite being set to remember 500 commands. However, the command file in ~/Library/Application Support/ChimeraX/commands contains (at least) 500 commands. Can you help? Alan

2 4

Unable to install boltz - please help
by Aggarwal, Aneel 25 Nov '25

25 Nov '25

Hello, I am a new user and trying to use boltz on my iMac (Tahoe OS) and get the error below. Any suggestions? Thanks, Aneel Successfully created Boltz Python virtual environment /Users/aneel/boltz22. Now installing Boltz and required packages from PyPi. This may take tens of of minutes since Boltz uses many other packages totaling about 1 Gbyte of disk space including torch, scipy, rdkit, llvmlite, sympy, pandas, numpy, wandb, numba... /Users/aneel/boltz22/bin/python -m pip install https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip Collecting https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip Using cached https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' INFO: pip is looking at multiple versions of boltz to determine which version is compatible with other requirements. This could take a while. ERROR: Could not find a version that satisfies the requirement torch==2.7.1 (from boltz) (from versions: 2.0.0, 2.0.1, 2.1.0, 2.1.1, 2.1.2, 2.2.0, 2.2.1, 2.2.2) ERROR: No matching distribution found for torch==2.7.1 [notice] A new release of pip is available: 24.0 -> 25.3 [notice] To update, run: /Users/aneel/boltz22/bin/python -m pip install --upgrade pip Boltz installation failed. See ChimeraX Log for details

3 5

Activation webcam macos sequoia MacBookAir M3 CimeraX 1.10
by GIUSEPPE DOMENICO TOCCHINI VALENTINI 25 Nov '25

25 Nov '25

Hello, I am trying to activate the webcam but I get the following message: [Screenshot 2025-11-25 alle 15.53.15.png] The application does not appear on the camera preferences/privacy. Do you have any suggestion? Thank you in advance. Giuseppe

2 1

Fwd: Boltz predictions and SMILES
by Eric Pettersen 25 Nov '25

25 Nov '25

> Begin forwarded message: > > From: Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> > Subject: RE: Your message to chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> awaits moderator approval > Date: November 25, 2025 at 8:19:02 AM PST > To: "chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>" <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> > > > Hi Guys, > This is about the behavior of smiles uploaded for boltz predictions. Some of the small molecule structures are incorrect after the predictions. My cyclohexyl ring was flattened to a benzene like ring; my protonated amine group in a benzyl amine ended up looking like a cyano group. Anything we can do about it? > Thanks > Krish > 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. >

2 1

Re: Problem with modeller execution location
by Alexandra Zahradnikova 24 Nov '25

24 Nov '25

Dear Vinita Now I see that the window I mentioned is not present when you run Modeller from your computer. Maybe you should first try a computation with the web service? I have never used a local installation of the Modeller. The licence key may bi different when working from inside ChimeraX. Best Sasha From: Alexandra Zahradnikova [mailto:alexandra.zahradnikova@savba.sk] Sent: Monday, November 24, 2025 10:13 To: 'Vinita Pant' Cc: chimerax-users(a)cgl.ucsf.edu Subject: RE: [chimerax-users] Re: Problem with modeller execution location Dear Vinita, In the menu item Structure Prediction/Model Loops or Modeller Comparative there are boxes in which you insert the license key (password) – see the screenshots. Best regards Sasha From: Vinita Pant [mailto:vinipant78@gmail.com] Sent: Saturday, November 22, 2025 18:26 To: Alexandra Zahradnikova Subject: Re: [chimerax-users] Re: Problem with modeller execution location Thank you for your response. However, I did not find any option to input the MODELLER password. Since I am not very tech-savvy, could you please guide me? Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943 On Sat, 22 Nov 2025 at 21:22, Alexandra Zahradnikova <alexandra.zahradnikova(a)savba.sk> wrote: Dear Vinita, You have to input the MODELLER password into the ChimeraX interface before starting the program. You will get the password by e-mail when you register with the Modeller web-page. Best Sasha From: Vinita Pant via ChimeraX-users [mailto:chimerax-users@cgl.ucsf.edu] Sent: Saturday, November 22, 2025 15:43 To: ChimeraX Users Help Subject: [chimerax-users] Re: Problem with modeller execution location Dear Elaine, I also tried reinstalling Modeller. But the problem persists. I have attached the image showing the error. Is there a way to manually fix this in Chimera? Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943 On Tue, 18 Nov 2025 at 22:41, Vinita Pant <vinipant78(a)gmail.com> wrote: Thank you for the clarification. Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943 On Tue, 18 Nov 2025, 10:39 pm Elaine Meng, <meng(a)cgl.ucsf.edu> wrote: The errror message is not about the path/location. It is about the license key, which you have to enter into the dialog directly. Please read the help: > https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html#key If you can't find the key in your local installation just follow the instructions/links in the above to get another key from the Modeller developers. Elaine > On Nov 18, 2025, at 8:59 AM, Vinita Pant via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Thank you for the information. Yes I have been using the academic version of Modeller directly. I tried locating the modeller path inside chimera. It still didn't work. > > Thanks and Regards > Vinita Pant > Doctoral Student (SRF) > ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal > Mobile No.: +91 9536940943 > > On Tue, 18 Nov 2025, 10:26 pm Elaine Meng, <meng(a)cgl.ucsf.edu> wrote: > Hi Vinita, > This error message is not about the location. As it says in the message, you have to get a license key for Modeller, which is obtained from the Modeller developers. > > This is all explained in the documentation, e.g. shown by clicking the Help button on the Model Loops dialog. See requirement #3 in the documentation: > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html#key> > > You would need to enter that license key into the tool as described. When you say "successfully using Modeller for homology modeling" I don't know if you meant from inside ChimeraX, or just using Modeller directly. If you were doing it from inside ChimeraX, you should have already gotten this license key and entered it into the ChimeraX dialog. If you were doing it directly with Modeller installed on your own computer, I don't know where the license key is kept. Probably somewhere in the Modeller installation. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Resource for Biocomputing, Visualization, and Informatics > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Nov 17, 2025, at 11:04 PM, Vinita Pant via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Dear ChimeraX Team, > > I am using ChimeraX (version: 1.10.1 (2025-07-24)) for filling missing residues, for which Chimera uses Modeller in the background. However, I've encountered an issue regarding the executable location of Modeller. Although I am successfully using Modeller for homology modeling, I am receiving a notification in ChimeraX stating that the license key is unavailable. I have attached an image of the error message for your reference. > > I would appreciate your guidance in resolving this matter. > > > > Thanks and Regards > > Vinita Pant > > Doctoral Student (SRF) > > ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal > > Mobile No.: +91 9536940943 > > _______________________________________________ > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

3 2

Thailand Real Estate
by soradath＠mailbox.in.ua 24 Nov '25

24 Nov '25

Real Estate in Thailand https://thailand-real.estate/

2 1

Re: Problem opening local small-molecule CIF file
by Starborg, Toby (RFI,RAL,BPSUP) 24 Nov '25

24 Nov '25

Oh dear. Sorry Ute, I'm afraid that I miss-read your original email. I was using the command open:ccd pim, which, I've just realised, you said worked. Sorry for the confusion. Out of interest where did you download the PIM.cif file and I will try opening it in the GUI. TobyS ________________________________ From: Ute Roehrig <Ute.Roehrig(a)sib.swiss> Sent: 24 November 2025 10:30 To: Starborg, Toby (RFI,RAL,BPSUP) <tobias.starborg(a)rfi.ac.uk> Subject: Re: Problem opening local small-molecule CIF file This is an external email. Please take care when clicking links or opening attachments. When in doubt, contact the helpdesk. Hi Toby, Which command is working for you? "open PIM.cif" does not work for me on linux/version 1.11.dev2025*, linux/version 1.10, macOS Tahoe/version 1.11.dev2025*, macOS Tahoe/version 1.10.1 Thanks, Ute ________________________________ From: Starborg, Toby (RFI,RAL,BPSUP) <tobias.starborg(a)rfi.ac.uk> Sent: Monday, November 24, 2025 10:56 To: Mailing List <chimerax-users(a)cgl.ucsf.edu>; Ute Roehrig <Ute.Roehrig(a)sib.swiss> Subject: Re: Problem opening local small-molecule CIF file Hi Ute, I'm by no means an expert, but I just tried the same command and it worked fine for me. Perhaps you need to expand the info to include what version of ChimeraX you are using and on what system? [FYI, I'm using version 1.10 on a Macbook Pro running Sequoia 15.7.1). TobyS ________________________________ From: Ute Roehrig via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> Sent: 24 November 2025 09:49 To: Mailing List <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] Problem opening local small-molecule CIF file This is an external email. Please take care when clicking links or opening attachments. When in doubt, contact the helpdesk. Hello, I'm having problems opening a locally stored small-molecule cif file. For example, the following runs without problems: open ccd:pim But if I download the file (PIM.cif) and try to open it with ChimeraX, I get an error: open PIM.cif -> No mmCIF models found. open PIM.cif format corecif -> No small molecule CIF models found. Perhaps this is a mmCIF file? open PIM.cif format smallcif -> No small molecule CIF models found. Perhaps this is a mmCIF file? Thank you in advance for your help, Ute

1 0

Problem opening local small-molecule CIF file
by Ute Roehrig 24 Nov '25

24 Nov '25

Hello, I'm having problems opening a locally stored small-molecule cif file. For example, the following runs without problems: open ccd:pim But if I download the file (PIM.cif) and try to open it with ChimeraX, I get an error: open PIM.cif -> No mmCIF models found. open PIM.cif format corecif -> No small molecule CIF models found. Perhaps this is a mmCIF file? open PIM.cif format smallcif -> No small molecule CIF models found. Perhaps this is a mmCIF file? Thank you in advance for your help, Ute

2 1

Re: Problem with modeller execution location
by Alexandra Zahradnikova 24 Nov '25

24 Nov '25

Dear Vinita, In the menu item Structure Prediction/Model Loops or Modeller Comparative there are boxes in which you insert the license key (password) – see the screenshots. Best regards Sasha From: Vinita Pant [mailto:vinipant78@gmail.com] Sent: Saturday, November 22, 2025 18:26 To: Alexandra Zahradnikova Subject: Re: [chimerax-users] Re: Problem with modeller execution location Thank you for your response. However, I did not find any option to input the MODELLER password. Since I am not very tech-savvy, could you please guide me? Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943 On Sat, 22 Nov 2025 at 21:22, Alexandra Zahradnikova <alexandra.zahradnikova(a)savba.sk> wrote: Dear Vinita, You have to input the MODELLER password into the ChimeraX interface before starting the program. You will get the password by e-mail when you register with the Modeller web-page. Best Sasha From: Vinita Pant via ChimeraX-users [mailto:chimerax-users@cgl.ucsf.edu] Sent: Saturday, November 22, 2025 15:43 To: ChimeraX Users Help Subject: [chimerax-users] Re: Problem with modeller execution location Dear Elaine, I also tried reinstalling Modeller. But the problem persists. I have attached the image showing the error. Is there a way to manually fix this in Chimera? Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943 On Tue, 18 Nov 2025 at 22:41, Vinita Pant <vinipant78(a)gmail.com> wrote: Thank you for the clarification. Thanks and Regards Vinita Pant Doctoral Student (SRF) ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal Mobile No.: +91 9536940943 On Tue, 18 Nov 2025, 10:39 pm Elaine Meng, <meng(a)cgl.ucsf.edu> wrote: The errror message is not about the path/location. It is about the license key, which you have to enter into the dialog directly. Please read the help: > https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html#key If you can't find the key in your local installation just follow the instructions/links in the above to get another key from the Modeller developers. Elaine > On Nov 18, 2025, at 8:59 AM, Vinita Pant via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Thank you for the information. Yes I have been using the academic version of Modeller directly. I tried locating the modeller path inside chimera. It still didn't work. > > Thanks and Regards > Vinita Pant > Doctoral Student (SRF) > ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal > Mobile No.: +91 9536940943 > > On Tue, 18 Nov 2025, 10:26 pm Elaine Meng, <meng(a)cgl.ucsf.edu> wrote: > Hi Vinita, > This error message is not about the location. As it says in the message, you have to get a license key for Modeller, which is obtained from the Modeller developers. > > This is all explained in the documentation, e.g. shown by clicking the Help button on the Model Loops dialog. See requirement #3 in the documentation: > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html#key> > > You would need to enter that license key into the tool as described. When you say "successfully using Modeller for homology modeling" I don't know if you meant from inside ChimeraX, or just using Modeller directly. If you were doing it from inside ChimeraX, you should have already gotten this license key and entered it into the ChimeraX dialog. If you were doing it directly with Modeller installed on your own computer, I don't know where the license key is kept. Probably somewhere in the Modeller installation. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Resource for Biocomputing, Visualization, and Informatics > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Nov 17, 2025, at 11:04 PM, Vinita Pant via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Dear ChimeraX Team, > > I am using ChimeraX (version: 1.10.1 (2025-07-24)) for filling missing residues, for which Chimera uses Modeller in the background. However, I've encountered an issue regarding the executable location of Modeller. Although I am successfully using Modeller for homology modeling, I am receiving a notification in ChimeraX stating that the license key is unavailable. I have attached an image of the error message for your reference. > > I would appreciate your guidance in resolving this matter. > > > > Thanks and Regards > > Vinita Pant > > Doctoral Student (SRF) > > ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal > > Mobile No.: +91 9536940943 > > _______________________________________________ > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

1 0

Problem with modeller execution location
by Vinita Pant 22 Nov '25

22 Nov '25

Dear ChimeraX Team, I am using ChimeraX (version: 1.10.1 (2025-07-24)) for filling missing residues, for which Chimera uses Modeller in the background. However, I've encountered an issue regarding the executable location of Modeller. Although I am successfully using Modeller for homology modeling, I am receiving a notification in ChimeraX stating that the license key is unavailable. I have attached an image of the error message for your reference. I would appreciate your guidance in resolving this matter. *Thanks and Regards* *Vinita Pant* *Doctoral Student (SRF)* *ICAR- Central Institute of Coldwater Fisheries Research, Bhimtal* *Mobile No.: +91 9536940943*

3 6

Chimera X with Apple Vision Pro
by Wolf, Inga 21 Nov '25

21 Nov '25

Dear Chimera X and Chimera developers, I'm a staff member of the Max-Planck-Institute of Biochemistry near Munich, Germany. At the moment we use Vive Pro virtual glasses to create a 3D picture of our biological structures that have extensions to be showed in Chimera X (.wrl, .mrc ...). Chimera X and the glasses can be connected. Vive Pro is now 8 years old and we think of buying Apple Vision Pro glasses. Can you please tell me if Chimera X or Chimera can talk to these glasses? Is there a possibility to see the structures in these glasses? Thank you in advance for your answer. Best regards, Inga Wolf Inga Wolf Cell and Virus Structure John Briggs [1685544407897] MAX PLANCK INSTITUTE OF BIOCHEMISTRY Am Klopferspitz 18 | 82152 Martinsried | Germany Phone: +49 (89) 8578 - 2634 iwolf(a)biochem.mpg.de<mailto:name@biochem.mpg.de> http://www.biochem.mpg.de/briggs<http://www.biochem.mpg.de/>

2 1

Predicting and modeling post-translationally modified C-terminal endings
by Parks, Ryssa 21 Nov '25

21 Nov '25

Hello, I am trying to predict and model a peptide docking to a receptor protein using ChimeraX's AlphaFold interface, and I was wondering if there is any way to specify post-translational modifications in the AlphaFold input function in ChimeraX? Our peptide has an amidated C-terminus, and my searches online have not yielded much success. Thank you, Ryssa Parks

4 9

Navigating to a OneDrive folder prompts a wholesale download
by David Bhella 20 Nov '25

20 Nov '25

Dear ChimeraX users and team, I am wondering if anyone can advise how to stop OneDrive trying to download the contents of every folder I navigate through when trying to e.g. save an image or open a file? I haven’t seen this behaviour with any other software, but as I maintain a lot of my work on OneDrive, it would be nice to be able to interact directly with the working folder. At the moment I need to work on a local folder and then copy files across when saving, and open files through finder rather than the ChimeraX dialog, otherwise my Mac locks up while it tries to download everything in every folder it sees. Thanks, D David Bhella Professor of Structural Virology Director, Scottish Centre for Macromolecular Imaging Associate Director, MRC - University of Glasgow Centre for Virus Research +44 (0)141 330 3685<tel:+441413303685> [cid:image002.png@01DAE420.99202CC0] [Logo, company name Description automatically generated]

2 1

AI spam
by Eric Pettersen 18 Nov '25

18 Nov '25

Hi all, We have made some further adjustments to try to prevent these AI spams posts you have seen over the last few days. We are hopeful, but you never can be sure... --Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

ChimeraX languages
by Nicolas Caudron - IA-IPR SVT 18 Nov '25

18 Nov '25

2 1

Emirates Estate
by soradae＠mailbox.in.ua 18 Nov '25

18 Nov '25

Real Estate in UAE https://emirates.estate/

1 0

Listing cavity contacting residues
by George Tzotzos 17 Nov '25

17 Nov '25

Hi everyone, I’ve used kvfinder and the command: coulombic (#1 & protein) surfaces #1.1.1 offset -1 select #!1 & (#!1.1.1 @< 3.5)185 atoms, 163 bonds, 34 residues, 1 model selected Is there a way to list the 34 residues? Have a good day George

2 2

Colouring a morph anim
by Pranav Shah 17 Nov '25

17 Nov '25

Hi Team, I am seeking advice on the most effective way to visualize a morphing trajectory within ChimeraX. Specifically, I have a multi-chain model transitioning (morphing) from its starting state to its final state, and I would like to know if there is a method in ChimeraX to apply a color gradient along this trajectory. Additionally, I would greatly appreciate guidance on how to color specific atoms, such as Cα atoms, based on their overall displacement. Ideally, the color intensity (hue) would increase in proportion to the magnitude of the displacement. Best regards, Pranav Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

2 2

Converting .stl to .mrc or .pdb
by mitchell.gulkis＠ufl.edu 17 Nov '25

17 Nov '25

Hello everyone, For instructional purposes, I am trying to generate simulated cryo-EM micrographs from a .stl file, in this case Mickey Mouse. This way, students can hold the 3D printed Mickey up to the micrograph to better understand projection images and angular assignment. I am able to open the .stl file in ChimeraX, but I can not figure out how to convert it to a format that is accepted by micrograph simulation programs, either .mrc or .pdb. Has anyone else figured out how to do this? Thanks! Sincerely, Mitch

4 3

On the web Casino wars 101 The way to Take full advantage of The Payout
by pachat71＠teleworm.us 16 Nov '25

16 Nov '25

On-line playing features speedily produced right multi-billion-dollar sector, giving fans worldwide enable you to employ in several playing pursuits through the convenience with their residences. This specific guidebook goals to deliver a wide check out on-line playing, protecting vital guidelines, powerful approaches, along with critical authorized concerns. No matter whether you happen to be a newcomer as well as a professional bettor, this information will assist you to understand the net playing panorama. Understanding On-line Betting https://khwin88.com/ On-line playing, often known as net playing as well as digital camera gaming, consists of setting gambling bets in several athletics, internet casino online games, as well as various other situations by way of on-line websites. These kind of websites, also known as sportsbooks as well as on-line casinos, present consumers which has a easy approach to position gambling bets, course his or her advancement, along with income out and about his or her income. Types involving On-line Betting Athletics Playing: This specific is just about the most favored varieties of on-line playing. Gamblers position wagers for the effects involving athletics situations, including basketball, hockey, soccer, along with mount sporting. Sportsbooks present different types involving gambling bets, which include moneyline gambling bets, place distributes, along with over/under gambling bets. Internet casino Online games: On-line casinos present numerous online games, which include casino wars, texas holdem, blackjack, roulette, along with baccarat. These kind of online games copy the feeling involving participating in in a very actual physical internet casino nevertheless are generally offered via just about any internet-connected unit. E-sports Playing: While using climb involving cut-throat video gaming, e-sports playing happens to be ever more popular. Gamblers could position wagers for the effects involving competitions along with suits throughout online games similar to Catego! ry involving Stories, Dota only two, along with Counter-Strike: World-wide Questionable. Wonderland Athletics: Wonderland athletics require generating personal squads involving true avid gamers along with rivalling versus various other squads using the players' real-life routines. Contributors position gambling bets on the wonderland squads, introducing yet another stratum involving enjoyment for you to classic athletics. Tips pertaining to Profitable On-line Betting Go with a Respected Playing Internet site: The first task throughout profitable on-line playing can be choosing a respected along with trusted playing internet site. Seek out internet sites which have been qualified along with managed by simply regarded specialists. Looking at testimonials along with checking out evaluations could also aid a stable podium. Recognize it can be: Focusing on how possibilities operate is extremely important to create advised playing judgements. Possibilities stand for your chance of an certain result along with ascertain your probable commission. Understand a variety of possibilities, including decimal, fractional, along with National possibilities. Deal with Your current Bank roll: Powerful bank roll operations is crucial for you to long-term good results throughout on-line playing. Collection a new afford your current playing pursuits along with stay with it. Stay away from going after cutbacks in support of gamble using income you'll be able ! to find the money for to shed. Shop around: Know-how can be electrical power in relation to on-line playing. Analysis squads, avid gamers, along with the latest routines to generate advised gambling bets. Being current using reports along with tendencies as part of your decided on playing place may give anyone a good edge. Employ Playing Approaches: Employing established playing approaches could enhance your current probability of earning. By way of example, throughout athletics playing, you could possibly employ approaches similar to price playing, wherever anyone discover gambling bets which may have a better chance involving earning as opposed to possibilities propose. Popular On-line Playing Strategies Sports Playing Strategies Price Playing: This tactic consists of figuring out gambling bets the place that the possibilities proposed by your bookmaker are generally above your chance in the result. By simply constantly acquiring price gambling bets, you'll be able to enhance your current probability of long-term productivity. Harmonized Playing: Harmonized playing consists of employing no cost gambling bets along with special offers proposed by sportsbooks to guarantee a new earnings. By simply setting a pair of the other gambling bets on a single celebration, you'll be able to deal with most probable effects along with risk-free a new earnings no matter the consequence. In-Play Playing: Often known as are living playing, this tactic consists of setting gambling bets through a celebration, in lieu of ahead of the idea commences. In-play playing permits you to reply to your unfolding activity along with perhaps come across additional beneficial possibilities. Casino Playing Strategies Martingale Technique: This is the common playing technique employed in online games similar to roulette along with blackjack. Your tactic consists of doubling your current gamble immediately after every single decline, using the essence retrieving most past cutbacks if you sooner or later get. Minute card Keeping track of: Throughout blackjack, minute card keeping track of may give anyone a bonus by simply tracking your playing cards that were put up. Even though minute card keeping track of can be authorized, it can be frowned about by simply casinos along with can bring about staying forbidden through the kitchen table. Slot machine Approaches: Even though casino wars are generally mainly determined by good luck, deciding on online games using larger commission percentages (RTP) along with being familiar with your paytable may help you make smarter judgements. E-sports Playing Strategies Are experts in One particular Sport: Paying attention on one e-sport may help you turn into an authority in this sport, supplying you with a greater idea of your squads, avid gamers, along with approaches engaged. This specific special know-how could boost your current playing judgements. Assess Crew Variety: Much like classic athletics, the contour along with functionality involving e-sports squads may vary. Inspecting the latest routines, gamer alterations, along with crew mechanics offers important remarks for ones gambling bets. Enjoy Are living Water ways: Seeing are living water ways involving e-sports situations could supply you with a real-time idea of the action along with enable you to location probable playing chances. Legal Concerns throughout On-line Betting Your legality involving on-line playing can vary commonly via land for you to land and in many cases within just instances of one particular land. It can be required to recognize your authorized panorama as part of your jurisdiction ahead of starting on-line playing. Regulations along with Licensing Licensing Specialists: Respected on-line playing internet sites can be qualified along with managed by simply regarded specialists, for example the BRITISH ISLES Casino Payment, your The island of malta Games Power, as well as your The state of nevada Games Command Aboard. These kind of the required licenses make sure sites work rather along with transparently. Get older Standards: Nearly all jurisdictions get get older standards pertaining to on-line playing, normally necessitating contributors to get at the least 19 as well as 11 years. Be sure you satisfy the authorized get older prerequisite as part of your place ahead of setting gambling bets. Levy Benefits: In most international locations, income via on-line playing could possibly be be subject to income taxes. It is vital to know your levy legal guidelines as part of your land along with survey your current income keeping that in mind. Responsible Gambling Dependable casino is often a vital element of on-line playing. Playing must be a sort of leisure, certainly not a means to generate profits. Here are several tricks for dependable casino: Collection Boundaries: Collection boundaries how much time along with income spent in playing. Adhere to these kind of boundaries and get away from going after cutbacks. Self-Exclusion: A lot of playing internet sites present self-exclusion possibilities, helping you to please take a separate via playing if you are it can be to become trouble. Seek out Support: In case you as well as a person you already know can be being affected by casino craving, seek out support via specialized companies including Gamblers Nameless as well as your Country wide Council in Trouble Casino. Choosing the correct On-line Playing Site Selecting the most appropriate on-line playing internet site is extremely important for the beneficial playing expertise. Here are several factors to consider: Reputation along with Trustworthiness Licensing along with Legislations: Guarantee the web page can be qualified by the respected power. Carefully consider home elevators your domain's licensing along with regulating system, generally observed end of it in the website. Reading user reviews: Looking at reading user reviews offers remarks in the domain's stability along with customer satisfaction. Seek out testimonials in unbiased websites to acquire the self-sufficient standpoint. Variety involving Playing Options Athletics along with Online games Presented: Go with a internet site which offers numerous playing possibilities, as well as your chosen athletics along with internet casino online games. Playing Market segments: Your availability of distinct playing market segments could increase your current playing expertise. Seek out internet sites that include various gamble varieties, including moneyline, distributes, along with brace gambling bets. Bonuses along with Promotions Delightful Signup bonuses: A lot of playing internet sites present delightful signup bonuses for you to bring in new customers. Assess your signup bonuses proposed by distinct internet sites to discover the ideal cope. On-going Special offers: Carefully consider on-going special offers along with commitment packages which could present more price after a while. Payment Methods Put in along with The Possibilities: Guarantee the web page sustains easy settlement methods the two tissue along with withdrawals. Common possibilities incorporate credit/debit playing cards, e-wallets, along with standard bank geneva chamonix transfers. Control Periods: Seek out internet sites using rapid control periods pertaining to tissue along with withdrawals to stop unwanted delays. Customer Support Access: Very good customer satisfaction is crucial pertaining to fixing just about any problems that may possibly happen. Seek out internet sites that include 24/7 assist by way of several routes, including are living chitchat, electronic mail, along with mobile phone. Responsiveness: Examination your responsiveness in the customer satisfaction crew by simply wondering a few questions ahead of joining. This will present you with a perception involving how much assistance you will probably have. Conclusion On-line playing comes with a stimulating along with easy approach to embark on several playing pursuits, via athletics along with internet casino online games for you to e-sports along with wonderland athletics. By simply being familiar with your a variety of on-line playing, employing powerful approaches, along with taking into consideration authorized along with dependable casino routines, you'll be able to increase your current playing expertise along with enhance your current probability of good results. You should go with a respected playing internet site along with often wager dependably. Satisfied playing!

1 0

PyPI Chimerax Package for Windows
by Berenice E Cowfer Chavez 14 Nov '25

14 Nov '25

Hello, Do you have a PyPI ChimeraX package for windows? I can online find a .whl file for macOS. Sincerely, Berenice E. Cowfer Chavez, M.S. Lab Manager, Profs. Johnson and Shoulders Labs Massachusetts Institute of Technology

2 1

A fixed clipping plane?
by jon_choy＠g.harvard.edu 14 Nov '25

14 Nov '25

Hi all, Prior to this I was an avid IMOD user. There I was able to set a clipping plane and move/rotate the model such that the model clipping plan would NOT clip any other parts of the model. Essentially i want to create a clipping plane, set it and then transform the model such that no other parts of the model will be clipped. Is this possible? I could not figure it out for the life of me. It's pretty simple in IMOD, just not sure if it's possible in ChimeraX. Would love to hear what you guys think. -Jon

4 6

color of capped surface
by stokes＠nyu.edu 12 Nov '25

12 Nov '25

I am having trouble with the surface color and specifically of capped surfaces. To start, surfaces of individual chains are given a single color, despite individual domains having been assigned a variety of colors. I can change the colors of the surface for individual domains subsequently, so that is not so bad. However, the color of the capped surface remains the initial color adopted when the surface was created. When I change colors of the individual chains, or domains, the surface color changes, but not the color of the capped/clipped surface. If I change the color of the entire model, then the surface cap changes. But it does not respond to subsequent changes of individual chains and domains. Hiding/showing the surface does not solve the problem (though I have a dim memory of this working in the past - maybe that was the old chimera). I am only using near/far clipping planes - not front/back. ChimeraX 1.10.1 on Ubuntu and 1.8 on Windows behave the same. Thanks in advance for any insight, David

2 2

Blurry Volume Rendering in ChimeraX ≥1.7 on macOS (HiDPI Regression Affecting ArtiaX)
by Yaroslav Tsytsyura 11 Nov '25

11 Nov '25

A little comment to the message: The following text was generated with help of an AI, because I’ve got frustrated trying to solve the issue myself and ran out of strength; I apologise for that. Yet it describes the problem well: Dear ChimeraX/ArtiaX developers, I would like to report an issue with volume rendering quality on macOS that appears to have been introduced in ChimeraX versions 1.7 and later, and that affects ArtiaX-based tomography workflows. System details macOS 26.0.1 on Apple Silicon (M2 Pro; RAM 16GB) ChimeraX 1.6.1 (works correctly) ChimeraX 1.7–1.10.1 (affected) ArtiaX 0.3 (works correctly) ArtiaX 0.6 (affected) Native ARM64 ChimeraX binary used (not via Rosetta) Tested both on the built-in display and external 4K monitor Issue summary When displaying reconstructed tomograms (binned 4x to pixel value 10A) in ChimeraX 1.7 and newer, the volume appears blurry, pixelated, and significantly lower in resolution compared to Fiji or ChimeraX 1.6.1. The same tomogram, same hardware, same display settings, and same scaling factors show correct high-quality sampling in ChimeraX 1.6.1 + ArtiaX 0.3. In contrast, ChimeraX ≥1.7 + ArtiaX ≥0.6 consistently produce a downsampled-looking rendering. Troubleshooting performed To rule out common macOS/Qt/HiDPI issues, I have tested: Forcing HiDPI mode (QT_ENABLE_HIGHDPI_SCALING, QT_SCALE_FACTOR, etc.) Launching via arch -arm64 Removing and reinstalling ChimeraX completely (including preferences) Disabling external 4K monitor scaling Resetting ChimeraX user settings None of these affected the outcome. Only reverting ChimeraX to version 1.6.1 restores correct rendering quality. Behavior differences observed In ChimeraX 1.6, tomograms appear crisp and match Fiji’s display quality. In ChimeraX 1.7–1.10.1, the same tomograms appear visibly blurred and pixelated. The command graphics quality high or similar parameters appear unsupported or ineffective in newer versions. ArtiaX toolbar loads but seems to use lower-resolution textures for slice volumes. This strongly suggests a rendering pipeline change around the transition from ChimeraX 1.6.1 → 1.7 that affects ArtiaX’s volume display on macOS (possibly due to Qt scaling, offscreen framebuffer size, or texture sampling changes). Request Could you please check whether: ArtiaX 0.6 is triggering half-resolution internal textures on macOS? The new rendering pipeline introduced in ChimeraX ≥1.7 affects HiDPI texture sampling? There is a fallback path on macOS ARM that reduces framebuffer resolution? Any configuration options can restore full-resolution sampling? To illustrate the difference between the two options (ChimeraX 1.6 vs 1.10.1) I have included the snapshots from two different M2 MacBooks running two different versions of ChimeraX/ArtiaX combinations; the tomogram file, tomogram optical slice position are the same, the screen magnification and the regions displayed are very similar. Thank you very much for your work and for looking into this. Best regards, Yaroslav ------------------------------------------- Dr. Yaroslav Tsytsyura Cellular Biophysics Institute of Medical Physics and Biophysics University of Muenster Robert-Koch Str., 31 48149, Muenster GERMANY phone: +49 251 8351 010 fax: +49 251 8355 121 Mobile: +49 157 895 47789 web-page: https://www.medizin.uni-muenster.de/impb/das-institut/elektronenmikroskopie…

2 2

Offscreen/headless render acceleration
by Roden Deng Luo 07 Nov '25

07 Nov '25

Hi, In https://www.cgl.ucsf.edu/chimerax/docs/user/options.html, under `--offscreen`, it says "It cannot use a graphics card or hardware-accelerated rendering because OpenGL does not support rendering without a window." I wonder if there are any possible ways to utilize graphics cards in the headless mode, or if you have any best practices for saving pictures/movies for hundreds to thousands of structures, with or without a GUI. Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

2 2

front-back shadow
by Citterico, Matteo 07 Nov '25

07 Nov '25

Hello, I’m having trouble changing the depth cue start and end settings in ChimeraX 1.8. I’ve tried several commands, but none of them seem to work. Could you please help me with this? Thank you in advance, Matteo

5 6

Recent spam
by Eric Pettersen 06 Nov '25

06 Nov '25

It seems that the era of AI bots signing up for and posting to mailing lists is upon us. I have banned the email address of the recent spam source and we are investigating methods to prevent these kinds of sign-ups/posts in the future. --Eric Eric Pettersen UCSF Computer Graphics Lab

2 1

The House Always Wins
by johncarry9t＠gmail.com 06 Nov '25

06 Nov '25

The word "casino" conjures specific imagery: the clinking of chips, the hypnotic spin of the roulette wheel, the electric chorus of a slot machine jackpot. For centuries, these establishments have been temples of chance, promising glamour, excitement, and the life-changing possibility of a big win. But behind the flashing lights and free-flowing cocktails lies a meticulously engineered ecosystem designed for one ultimate goal: profitability. The modern casino is a fascinating blend of psychology, architecture, technology, and entertainment, far removed from the smoky, simplistic gambling halls of the past. https://hamiltongardens.org/visit/ The Architecture of Addiction: Designed to Disorient From the moment you step inside, the casino environment is carefully crafted to keep you playing. There are no clocks or windows, creating a timeless bubble where the outside world ceases to exist. Labyrinthine floor plans encourage exploration and make it difficult to find the exit. The air is oxygenated to keep patrons alert, and the constant sensory stimulation—from the ringing of slots to the vibrant carpet patterns—creates an atmosphere of thrilling chaos. This design is no accident. It's a calculated strategy to maximize "time on device." The longer a guest stays, the more the mathematical advantage of the games, known as the "house edge," grinds down their bankroll. Every element, from the placement of popular slots to the complimentary "comps" like drinks and hotel rooms, is a tool to enhance customer retention. The Games: A Calculated Dance of Chance At its core, a casino's business model is a masterpiece of applied mathematics. Every game offered is statistically tilted in the house's favor. Slot Machines: The undisputed king of the casino floor, slots are now sophisticated computers. Their outcomes are determined by Random Number Generators (RNGs), and their payout percentage, or "Return to Player" (RTP), is programmed in advance. Their appeal lies in their simplicity and the potential for massive, albeit infrequent, jackpots. Table Games: Games like Blackjack, Roulette, and Baccarat offer more player agency, but the house edge is immutable. In Blackjack, the dealer plays by fixed rules that disadvantage the player over time. In Roulette, the presence of the "0" and "00" on the American wheel gives the house its built-in advantage. Craps and Baccarat operate on similar statistical principles. Despite the odds, these games thrive because they offer the illusion of control and the social spectacle of a live game, presided over by a skilled dealer. Beyond the Floor: The Rise of the Integrated Resort The 21st-century casino is rarely just a casino. The model of the "Integrated Resort" has transformed these venues into full-scale entertainment destinations. Today's major casinos are home to: World-class hotels and spas Celebrity-chef restaurants High-end retail shopping Arena-sized theaters hosting A-list performers Convention and meeting spaces This diversification is a strategic move. By attracting conventioneers, gourmands, and concert-goers who may not be primary gamblers, resorts ensure a steady revenue stream that isn't solely dependent on the volatility of the gaming floor. It normalizes the casino, repositioning it as a legitimate vacation spot for a broader demographic. The Digital Frontier: Online Casinos and the Future The most significant shift in recent years has been the explosive growth of online casinos and mobile sports betting. The digital realm removes all physical barriers, allowing people to gamble from their living rooms or on their phones. This presents both immense opportunity and significant challenges. Online platforms use sophisticated algorithms and bonus structures to engage players, often with even higher efficiency than their brick-and-mortar counterparts. This accessibility has intensified the focus on responsible gambling. Regulators and ethical operators are now implementing tools like deposit limits, "cool-off" periods, and self-exclusion programs to help mitigate the risks of addiction that are amplified in the always-available online environment. The Final Bet The modern casino is a complex entity. It is a source of employment, tourism revenue, and entertainment for millions. It is also a highly engineered environment that profits from human psychology and mathematical certainty. As the industry continues to evolve with technology and expand into new markets, the balance between entertainment, profit, and social responsibility remains its defining tension. The house may always win in the end, but understanding the intricate machinery behind the magic curtain is the most valuable bet a visitor can make.

1 0

F8BET Payment Methods
by johncarry9t＠gmail.com 06 Nov '25

06 Nov '25

A seamless banking experience is F8BET essential for any online casino player. F8BET provides a variety of safe, fast, and convenient payment methods, ensuring that deposits and withdrawals are hassle-free. Whether you prefer credit cards, e-wallets, or cryptocurrencies, F8BET guarantees secure transactions so you can focus on gaming. https://f8betlv.com/ Why Payment Methods Matter Efficient payment options enhance your online casino experience by: Saving Time: Quick deposits and withdrawals mean more gameplay. Providing Security: Advanced encryption protects your financial information. Offering Flexibility: Multiple options cater to different player preferences. Enabling Bonuses: Many payment methods qualify for deposit promotions. Deposit Options at F8BET F8BET offers multiple deposit methods for player convenience: 1. Credit and Debit Cards Visa, MasterCard, and Maestro are widely accepted. Instant deposits with secure processing. Tip: Ensure your card is enabled for online transactions. 2. E-Wallets Options include Skrill, Neteller, and ecoPayz. Quick deposits with added privacy. Tip: Some e-wallets offer cashback or promotions when depositing. 3. Bank Transfers Direct transfers from your bank account. Reliable and secure, though processing may take longer than e-wallets. 4. Cryptocurrencies Bitcoin, Ethereum, and other popular cryptocurrencies are accepted. Fast and secure with added anonymity. Tip: Check current exchange rates to maximize your deposit value. Withdrawal Methods F8BET ensures smooth and Đăng ký F8BET timely withdrawals: https://f8betlv.com/ E-Wallets: Typically processed within 24 hours. Bank Transfers: May take 2-5 business days depending on your bank. Credit/Debit Cards: Usually processed within 1-3 business days. Cryptocurrency: Withdrawals are fast, often completed within a few hours. Security Measures F8BET prioritizes player safety: SSL Encryption: Protects all financial and personal data. Verified Transactions: Each deposit and withdrawal is monitored for security. Trusted Payment Partners: F8BET works with reputable financial providers. Tips for Smooth Transactions Verify Your Account: Complete KYC (Know Your Customer) to avoid delays. Check Minimums and Maximums: Each payment method has specific limits. Use the Same Method for Deposit and Withdrawal: Ensures faster processing. Monitor Your Bank Statements: Keep track of transactions to avoid errors. Contact Support if Needed: F8BET customer service is available 24/7 for banking issues. Mobile Banking Convenience F8BET’s mobile platform supports all deposit and withdrawal methods. Manage your funds directly from your smartphone or tablet. Mobile banking maintains the same security and speed as desktop transactions. Conclusion Safe and fast banking is a key part of an enjoyable online casino experience, and F8BET excels in this area. With multiple deposit and withdrawal options, advanced security measures, and efficient processing, players can focus on slots, table games, and live casino action without worrying about payments. By following simple tips like account verification, tracking transactions, and using consistent payment methods, you can enjoy a smooth banking experience every time. Deposit, play, and withdraw with confidence at F8BET—your secure online casino destination!

1 0

confirm
by 汪洋 05 Nov '25

05 Nov '25

 confirm c28d09cf0893ee23fc780e120106b9b266ea0623

1 0

ChimeraX VR (specifically LookSee)
by jrj.healey＠gmail.com 02 Nov '25

02 Nov '25

Hi all, I'm trying to get ChimeraX VR standalone working on a Quest 3. Trying to follow the instruction online, but I fall at pretty much the first hurdle trying to subscribe to the release candidate channel on Meta AppLab - I get an error saying the channel is out of date or can no longer be found (or something to that effect). Do you have any more information on this, and does this mean side-loading is my only option potentially? Thanks Joe

3 2

What is the University of Michigan manufacturing partnership with LS Manufacturing?
by altabunny9_at_gmail.com＠mail.d2l.msu.edu 01 Nov '25

01 Nov '25

In today’s rapidly evolving industrial landscape, the manufacturing sector stands at the intersection of innovation and technology. From 3D printing (additive manufacturing) to CNC machining (subtractive manufacturing), modern engineers are required to bridge the gap between theory and real-world application. Recognizing this growing need, the University of Michigan’s College of Engineering has established a ground-breaking partnership with LS Manufacturing, a leading global on-demand manufacturing company. This collaboration—centred around the University of Michigan manufacturing partnership initiative—aims to provide students with hands-on experience in additive and subtractive manufacturing education, bridging academic theory with real-world industrial practices. Together, they are shaping the next generation of manufacturing engineers, innovators, and entrepreneurs. <ol> <li>Introduction</li> </ol> Manufacturing today is not just about producing parts; it’s about producing ideas, efficiency, and sustainability. The rise of additive manufacturing technologies such as 3D printing, alongside traditional subtractive manufacturing methods like CNC machining, has transformed how engineers design, test, and create. Yet, one challenge remains constant in academia—how can students gain real-world manufacturing experience before entering the workforce? Hands-on education is crucial to understanding how concepts like material tolerances, design for manufacturability (DFM), and prototyping translate from theory into production. To address this, the University of Michigan Engineering Department, in partnership with LS Manufacturing, launched a forward-thinking initiative to blend classroom learning with industrial collaboration. This partnership emphasizes rapid prototyping for academic research, student project sponsorship in CNC machining, and opportunities for real-world manufacturing experience for students through capstone project sponsorships and innovation-focused technical grants. <ol start="2"> <li>The Partnership’s Vision & Goals</li> </ol> The University of Michigan manufacturing partnership with LS Manufacturing was born from a shared vision: to cultivate a new generation of engineers fluent in both the digital and physical realms of production. Goal 1: Enhance Student Learning At its core, the partnership focuses on improving how students learn and apply manufacturing principles. By providing access to industrial-grade manufacturing equipment, students can design, prototype, and refine projects using professional tools like high-precision CNC machines and advanced 3D printers. This approach transforms the University of Michigan’s classrooms and labs into dynamic, industry-connected learning environments. Students don’t just learn about manufacturing—they experience it firsthand. Goal 2: Bridge Theory and Practice Engineering theory provides the foundation for design, but practice makes it meaningful. Through this partnership, students engage directly with industry partners from University of Michigan Engineering and LS Manufacturing experts. They receive practical insights into design for manufacturability (DFM), rapid prototyping, and low-volume production—critical skills that align with modern industry expectations. For instance, when developing prototypes, students can leverage rapid prototyping for academic research, gaining experience in both additive and subtractive processes. This real-world engagement ensures they are not only technically proficient but also ready to innovate efficiently. Goal 3: Foster Innovation Innovation thrives at the intersection of creativity and capability. The University of Michigan partnership supports student-led initiatives such as the Solar Car Team, Robotics Club, and Formula SAE by providing manufacturing expertise, technical feedback, and production services. From concept sketches to final assembly, LS Manufacturing’s involvement helps these teams iterate faster and smarter. This collaboration empowers students to push the boundaries of engineering innovation while gaining the confidence to lead future industry breakthroughs. <ol start="3"> <li>How the Partnership Works: The “LS Manufacturing Technical Grant”</li> </ol> At the heart of this collaboration lies the LS Manufacturing Technical Grant, a unique sponsorship-in-kind program designed to empower student innovation. Through this grant, LS Manufacturing offers selected University of Michigan student projects and faculty research initiatives a combination of expert DFM feedback, rapid prototyping services, and production support using state-of-the-art CNC machining, 3D printing, and injection molding technologies. This model represents a corporate sponsorship in manufacturing that prioritizes educational value and accessibility. Rather than a traditional cash grant, it provides students with tangible, high-impact resources—professional-grade components, real-time consultation, and access to global production networks. Application Process The process is simple and inclusive. Student teams, faculty members, or research labs can apply through the University of Michigan Engineering Department’s partnership portal. Applicants outline their project goals, design needs, and desired manufacturing processes. Selected participants receive LS Manufacturing’s technical support to bring their designs to life. This initiative promotes student project sponsorship in CNC machining and similar technologies, encouraging students to prototype and test ideas efficiently. It’s a hands-on, learning-by-doing opportunity that merges academic ambition with industrial capability. <ol start="4"> <li>Expected Impact & Benefits for UM Students</li> </ol> The collaboration’s impact extends far beyond the classroom. It delivers a transformative learning experience by combining advanced technology, mentorship, and real-world exposure. Access to Global Manufacturing Networks Through LS Manufacturing’s online instant quoting platform, students gain access to a vast global manufacturing network. They can upload designs, receive cost estimates instantly, and understand how design choices affect pricing and feasibility. This mirrors real-world industry practices, preparing them for professional engineering roles where digital manufacturing tools are essential. Reduced Project Costs and Lead Times Student projects often face challenges such as limited funding and long turnaround times. LS Manufacturing helps address both issues by providing cost-effective production support and faster lead times. Whether it’s producing a prototype for a capstone project or components for research testing, students can move from concept to prototype at record speed. Skill Development and Industry Interaction Beyond technical proficiency, this partnership develops professional skills—teamwork, communication, and project management. Students interact directly with LS Manufacturing’s engineering experts, gaining feedback on design feasibility and manufacturing optimization. Such exposure provides a window into real-world manufacturing experience, helping them bridge the often-cited gap between academia and industry. Accelerated Research and Innovation For faculty and graduate researchers, access to LS Manufacturing’s rapid prototyping services means faster testing and iteration cycles. Projects that once took months to prototype can now progress in weeks, enabling researchers to focus more on innovation and less on logistical barriers. Ultimately, this partnership enhances not just student outcomes, but the entire research ecosystem at the University of Michigan. <ol start="5"> <li>About LS Manufacturing</li> </ol> LS Manufacturing is a global leader in on-demand manufacturing and rapid prototyping services, empowering innovators and engineers to move from prototype to production with speed and precision. Their core capabilities include CNC machining, 3D printing, injection molding, and sheet metal fabrication—making them a one-stop solution for any stage of the manufacturing process. Through collaborations with academic institutions, LS Manufacturing demonstrates its commitment to supporting education, innovation, and workforce development. By working with the University of Michigan, the company is investing in the future of engineering talent and helping shape the next generation of manufacturing leaders. To learn more about their services and mission, visit <a class="external" href="http://www.lsrpf.com" target="_blank" rel="noreferrer noopener">www.lsrpf.com</a>. <ol start="6"> <li>Conclusion & Looking Ahead</li> </ol> The partnership between the University of Michigan and LS Manufacturing exemplifies what’s possible when academia and industry work hand in hand. By merging additive and subtractive manufacturing education with real-world applications, the collaboration equips students with the tools, experience, and confidence to lead the future of manufacturing. Through the LS Manufacturing Technical Grant, University of Michigan students are not only designing innovative products but also learning how to manufacture them efficiently—a skill set that’s indispensable in the global economy. As this partnership continues to grow, it promises to inspire new research collaborations, support entrepreneurial initiatives, and redefine how engineering education meets the demands of modern manufacturing. The future of the industry depends on creative thinkers, hands-on problem solvers, and innovators—and this program ensures they’re ready to lead. <ol start="7"> <li>Call to Action (For the UM Audience)</li> </ol> Faculty and student teams interested in exploring manufacturing innovation or applying for the LS Manufacturing Technical Grant are encouraged to contact the University of Michigan College of Engineering Department of Mechanical Engineering or visit the UM Engineering Partnership Page for more information. This is more than a sponsorship—it’s a movement toward redefining how students learn, design, and build. Together, the University of Michigan and LS Manufacturing are crafting the future of engineering education—one prototype at a time. FAQs <ol> <li>What is the University of Michigan manufacturing partnership with LS Manufacturing?</li> </ol> The University of Michigan manufacturing partnership with LS Manufacturing is a collaborative program designed to give students hands-on experience in modern manufacturing technologies. It combines additive (3D printing) and subtractive (CNC machining) education, helping students bridge the gap between classroom learning and real-world industrial practice. <ol start="2"> <li>How does the LS Manufacturing Technical Grant benefit University of Michigan students?</li> </ol> The LS Manufacturing Technical Grant provides selected students and faculty projects with in-kind sponsorship. This includes DFM (Design for Manufacturability) feedback, rapid prototyping services, and production support using advanced manufacturing technologies. It reduces project costs, shortens lead times, and gives students direct access to industry-level expertise. <ol start="3"> <li>Who can apply for the LS Manufacturing Technical Grant at the University of Michigan?</li> </ol> The grant is open to University of Michigan students, faculty members, and research teams involved in academic or innovation-based projects. Applications can be submitted through the University of Michigan Engineering Department’s partnership portal, detailing project goals and manufacturing requirements. <ol start="4"> <li>What kind of real-world experience do students gain through this partnership?</li> </ol> Students gain real-world manufacturing experience by collaborating directly with LS Manufacturing engineers, learning about design for manufacturability, rapid prototyping, and low-volume production. They also gain exposure to digital tools like instant quoting platforms and online manufacturing networks, preparing them for careers in modern industry. <ol start="5"> <li>How can faculty or student teams learn more about the LS Manufacturing partnership?</li> </ol> Interested participants can visit the University of Michigan College of Engineering’s Partnership Page or contact the department directly for detailed program information. The page includes application guidelines, eligibility details, and examples of past capstone project sponsorships supported by LS Manufacturing.

1 0

Further help
by Emily Cioppa 29 Oct '25

29 Oct '25

Good evening, In addition to my previous question, I am also having difficulty appending chains. If I import molecular models into Chimera/ChimeraX that each have individual model names and singular Chain IDs, is there a way to combine these into a singular model and renumber the residues as one continuous sequence throughout the combined model? For example, I have three molecular models that are each components of a single RNA molecule, and each have their own pdb file and a singular Chain ID. I know how to physically orient all of them spatially and renumber the residues of each such that when hovering over the molecular model moving from 5’ to 3’ the sequence numbering is continuous and correct across all chains. However, even when I combine the three individual models into one at the beginning and change the chain IDs of all three to be the same ID at the end, when I view the combination model in sequence viewer, it has just appended all three chains together with no regard to residue order. Since each of the three models is a chunk of double helix, I would need the numbering to be in 5’ to 3’ order throughout the entire combination model sequence viewer, in the way that I have renumbered it and in the way that it is in the visible combined model/structure. Thank you for your help.

2 1