- Chimera-dev - RBVI Mailing Lists

Issue debugging on windows with bundle_builder_toml.py
by Lou Holland 06 Mar '26

06 Mar '26

Hello, I'm afraid I have another problem (still seemingly windows related). I have been updating to use the pyproject.toml build system (as well as making my bundle depend on chimerax.clipper for most of my precompiled libraries etc). As usual, it builds fine on mac but doesn't on windows, however I'm having hard time figuring out why. I'm building from within ChimeraX 1.11.1 (previously I was using 1.10.1 but the chimerax.clipper version I need requires 1.11.1). It seems to get through most of the stages, copying over files etc to the build folder, but then fails with the error message: > running build_ext > Traceback (most recent call last): > File "C:\Users\lah583\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\core\commands\devel.py", line 180, in _run unbound_method(bb, *args, **kw) > File "C:\Users\lah583\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\bundle_builder\bundle_builder_toml.py", line 572, in make_install > wheel = self.build_wheel() > ^^^^^^^^^^^^^^^^^^ > File "C:\Users\lah583\AppData\Local\Programs\ChimeraX 1.11.1\bin\Lib\site-packages\chimerax\bundle_builder\bundle_builder_toml.py", line 878, in build_wheel > self.version = dist.get_version() > ^^^^^^^^^^^^^^^^ > AttributeError: 'NoneType' object has no attribute 'get_version' My guess would be that _run_setup() is failing, but the problem I'm having is that, unlike when building from bundle_builder.py where run_setup prints any exceptions, when using the .toml system it doesn't seem to tell me what went wrong. I just know that it clearly failed to produce dist from the fact that dist is still NoneType. Apologies if I'm missing something obvious in terms of how to run it in debug mode. I've been running ChimeraX - Console (1.11.1) as I can't see a ChimeraX - Debug for 1.11.1. Best wishes, Lou Holland (Pronouns: they/them) Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK

2 1

New ChimeraX Plugin: Cube'n Tube
by Cairoli Tamino 24 Feb '26

24 Feb '26

Hey all, I’m happy to share a small plugin I recently developed for UCSF ChimeraX: Cube’n Tube. It extends the standard eraser sphere tool. Instead of only a sphere, you can now erase with cubes, cylinders (frustum), cones, or even define your own custom shape. While working with various protein structures, I often felt that a spherical eraser is not always ideal. Especially when trying to remove part of a filament, micelle density, or isolate one asymmetric unit of a larger assembly. I was really missing a more dynamic eraser tool, so I decided to build it. I also implemented a simple undo/redo function for the eraser tool. I cannot count how often I misclicked and had to restart my masking from zero… Now there is a one-step undo (limited to one step to keep it smooth on all machines). The custom shape option works particularly well together with a fitted atomic model (for example from AlphaFold) to erase everything outside the region of interest. Cube’n Tube can be downloaded directly from the ChimeraX Tool Shed or from GitHub (https://github.com/TaminoCairoli/CubeNTube) If you are missing a feature or have ideas for improvements, feel free to open an issue on GitHub. Many thanks to the team (especially Tom Goddard) at University of California, San Francisco for building such a powerful and well-documented tool, and thanks to Pavel Afanasyev, Julius Rabl and Dianhong Wang for discussion and testing. Best, Tamino

1 0

Compiling bundles on Windows error LNK2001 for python functions
by Lou Holland 19 Feb '26

19 Feb '26

Hello, I have successfully compiled and tested my Privateer for ChimeraX bundle on MacOS and Linux but am having issues trying to compile on Windows. I apologise in advance if my questions are naive or silly; I feel like a complete beginner when it comes to developing in the Windows environment. Following the guide here ( https://www.cgl.ucsf.edu/chimerax/docs/devel/environment.html) I ensured I have Visual Studio 2019. I tried compiling in Visual Studio directly using a make_win.bat file. I also tried installing MinGW and installing the necessary packages with pacman (as outlined in the guide) and compiling from there using a standard Makefile. In both cases I get the same issue, whereby all my C++ library dependencies compile, and my own C++ code compiles into .obj files, but when it comes to building the wheel, it fails due to linker errors (LNK2001: unresolved external symbol) which all seem linked to Python (e.g. error LINK2001: unresolved external symbol __imp__PyThread_tss_create and many more similar ones too) and relate to the .obj file for the C++ file which contains the python bindings with pybind11. I tried explicitly adding a link argument to python311.lib in case that was the issue, but it didn't help. I do not have this issue on MacOS or on LInux. I was just wondering if this is something anyone else has come across or can point me in the right direction. Any help is much appreciated. Best wishes, Lou Holland (Pronouns: they/them) Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK

3 3

[UNIGE] Chimera Request
by RENZULLI Giuseppe 04 Apr '25

04 Apr '25

Good Morning, I'm a cloud engineer for Sopra Steria, and I would like to know more about your software Chimera. We are distributing your software through Intune, but we are having problems with the install and uninstall strings, possibly even for a silent mode. Thank you very much in advance, Have a nice day Giuseppe RENZULLI Senior Cloud Consultant [Sopra Steria] Via Camporeale - 83031 Ariano Irpino (AV) giuseppe.renzulli(a)soprasteria.com<mailto:giuseppe.renzulli@soprasteria.com> - www.soprasteria.it LinkedIn<https://www.linkedin.com/company/soprasteria> | X<https://twitter.com/SoprasteriaIT> | Facebook<https://www.facebook.com/soprasteriaitalia> | Instagram<https://www.instagram.com/soprasteriaitalia/?hl=it> [cid:image002.png@01DBA54A.FB151F30]<https://www.bestworkplaces.it/aziende/soprasteria/> Questo messaggio può contenere informazioni riservate, la cui divulgazione è rigorosamente vietata senza l'esplicita autorizzazione del mittente. Qualora questo messaggio sia stato ricevuto per errore, si prega di rinviarlo al mittente e di distruggerne ogni copia. Gli allegati a questa e-mail sono stati oggetto di un controllo antivirus. Tuttavia, non ci assumiamo alcuna responsabilità per danni causati da eventuali virus. P Please consider the environment - Do you really need to print this email? C2 - Uso Limitato

2 1

Bundle development for chimeraX - svg onClick event to run command from QWebEngineView
by Lou Holland 18 Feb '25

18 Feb '25

Hello, I am currently working on a privateer bundle for carbohydrate validation in chimeraX. At present, I have it so that the privateer tool will display SNFGs of glycans present in the structure using svgs displayed in a QWebEngineView(). I would like, if possible, on clicking elements of the svg to run a chimeraX command (view /chainID:resID) to centre the view window on the residue in question. At present, I can implement an onClick event to display the command that should be run, but haven't managed to figure out how to just run the command from within that QWebEngineView. Is there a mechanism already in place for doing something like this that I could take advantage of? I'd considered using the "log html" to display the svgs in the log instead of the WebEngineView() so that I could take advantage of the href="cxcmd" functionality, but the svgs are long, with semicolons and new-line characters which interfere with this. Best wishes, Lou Holland (Pronouns: they/them) Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK

2 2

Chimera 1.X PDB downloads are broken
by Jeremy Henry 12 Feb '25

12 Feb '25

Hello Chimera team, FYI, this morning we switched the backend file serving at RCSB Protein Data Bank to a newer service. In viewing our logs we have noticed that Chimera 1.X is using http/1.0 POST to pull the files, which is now broken due to more restrictive policies we have in place compared to our previous service. Using GET should still work with http/1.0. I'm not sure what ChimeraX uses, but that seems to be working fine. Shall I direct our support team to recommend users switch to ChimeraX if we get asked? Thanks and regards, Jeremy Henry DevOps Engineer RCSB Protein Data Bank UC San Diego

2 2

Command to "reinstall" a plugin?
by Rocco Moretti 10 Feb '25

10 Feb '25

Hello, The instructions at https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/introduction.html#bu… talk about how to build and install a bundle plugin (with the "devel build" and "devel install" commands). However, I notice that executing these commands doesn't necessarily reflect the changes I'm making to the plugin I'm actively developing. (The changes I make to the source code don't take effect in ChimeraX.) -- I've figured out that to make the changes show up, I need to execute `toolshed uninstall` first, prior to `devel install`. (I've also noticed that it seems like a separate `devel build` step isn't needed if you are running `devel install`, which is not clear from the documentation.) Is there something like a `devel reinstall` command which will do this for me in a single command? That would make doing things like iterative debugging a bit easier. -- Or am I potentially doing something wrong with how I'm running the install command. Thanks, Rocco

3 2

Thread_safe REST Api call
by Simon Dürr 09 Oct '24

09 Oct '24

Hi, I'm currently developing a chimerax extension that makes a REST Api call using the gradio_client library: Here is a minimal working example (using gradio_client==1.4.0) from gradio_client import Client from chimerax.core.commands import run def print_result(self, results): results[1] is a path to a local file run(self.session, f"open {results[1]}") client = Client("https://mlsb-demo-plinder-smina.hf.space/") result = client.submit( input_sequence="", input_ligand="COc1ccc(cc1)n2c3c(c(n2)C(=O)N)CCN(C3=O)c4ccc(cc4)N5CCCCC5=O", input_protein=handle_file('https://huggingface.co/spaces/MLSB/demo_plinder_smina/raw/main/input_test.p…'), exhaustiveness=1, api_name="/predict", result_callbacks=[print_result] ) However, when I try to open the loaded file in ChimeraX after the prediction is finished and the callback is run I get the following error: RuntimeError: Attempted to make OpenGL context current in wrong thread (26408, context thread 21820). I presume I need to use a Task like here to run the chimerax.core.commands.run in the same thread as the ui. https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/core/tasks.html Are there any minimal examples how to do this or other suggestions how to make this work? Thanks, Simon Dürr https://simonduerr.eu<https://simonduerr.eu/>

2 1

Example Bundle links broken
by Simon Dürr 11 Sep '24

11 Sep '24

Dear Chimera Developers, it seems the example source code download links are broken in the documentation: https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_tool_qt.html All links have the format as below and don't work http://www.rbvi.ucsf.edu/chimerax/cgi-bin/bundle_tutorial.zip?name=tut_tool… Could you fix this or point me to the correct location for the download? Thank you Simon Dürr

2 1

chimera stereo anaglyph implementation
by Jonas Hiltmann 12 Jun '24

12 Jun '24

Dear madam, dear sir, I am trying to write a bundle for ChimeraX that includes the possibility to apply an anaglyph (red-cyan) filter to a model. It has come to my attention that this function had already been featured in chimera but not in chimerax. I have been trying to find how it has been implemented in the chimera sourcecode but have not been successful. I found the method declaration in the include/_chimera/stereo.h file but not the code that defines the logic. If you could help me find it I would greatly appreciate it. This is in the context of a research project of the Hochschule Bonn-Rhein-Sieg. Yours sincerefuly, Jonas Hiltmann

2 2