February 2025 - Chimera-dev - RBVI Mailing Lists

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

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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

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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

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