Dear ChimeraX Users, I'm currently working on a bundle for building lipid membranes and I have a few questions: 1. A part of my bundle is a lipid selector that works with AMBER-compatible pdb files. I followed the tutorial and have successfully built a selector that selects all lipids of the type I specify (say, I put in the command line 'sel POPC' then all the POPCs in the membrane get highlighted). Because of the way AMBER lipid forcefields work, individual lipids are separated into three residues, one head and two tails. I'm trying to add a function to my bundle such that individual lipids can be selected - e.g. when I select a headgroup and go [up]+[up], then the entire lipid can be selected. How can I group three residues together in a bundle? 2. Is it possible to register multiple selectors through a single function? There are many lipids that I want to include in the selector, but for now I have to copy the same function over and over if I want to do that. It will be great if I could have a list containing all the names of the lipids and have a function that registers all of them. 3. Are there any built bundles that are open source? I tried to access the source code of bundles after installing them but I couldn't find the directory of which they are stored. It will be really helpful if I could refer to them. Thank you so much for your help! Best Regards, Katie
Katie, 1. I don't know 2. Yes, I've done this in my SEQCROW bundle. It'll probably depend on how you can organize the code. You can see my code here (sorry it doesn't have many annotations): https://github.com/QChASM/SEQCROW/blob/5a5d00f2d6368a68dca8abcb7e816b7ac1202.... Basically, calling register_selector from chimerax.core.commands will add a new selector. I pass a lambda function with different default values for a keyword argument to register_selector. The behavior of the function in the lambda changes based on the value of this keyword argument. I do this to register the selectors for substituents, atoms with a particular VSEPR shape, and a few other identifiers. 3. Open-source bundles have a green keyhole symbol at the top of their bundle page. Clicking that should take you to the code repository on GitHub or wherever. The install folder depends on your operating system. On Windows, it's in %userprofile%\AppData\Local\UCSF\ChimeraX\(version)\site-packages Best, Tony 1. 2. ________________________________ From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Zeng, Katie via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Tuesday, February 1, 2022 1:21 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Building ChimeraX Bundle [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Dear ChimeraX Users, I'm currently working on a bundle for building lipid membranes and I have a few questions: 1. A part of my bundle is a lipid selector that works with AMBER-compatible pdb files. I followed the tutorial and have successfully built a selector that selects all lipids of the type I specify (say, I put in the command line 'sel POPC' then all the POPCs in the membrane get highlighted). Because of the way AMBER lipid forcefields work, individual lipids are separated into three residues, one head and two tails. I'm trying to add a function to my bundle such that individual lipids can be selected - e.g. when I select a headgroup and go [up]+[up], then the entire lipid can be selected. How can I group three residues together in a bundle? 2. Is it possible to register multiple selectors through a single function? There are many lipids that I want to include in the selector, but for now I have to copy the same function over and over if I want to do that. It will be great if I could have a list containing all the names of the lipids and have a function that registers all of them. 3. Are there any built bundles that are open source? I tried to access the source code of bundles after installing them but I couldn't find the directory of which they are stored. It will be really helpful if I could refer to them. Thank you so much for your help! Best Regards, Katie
On Feb 1, 2022, at 10:21 AM, Zeng, Katie via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Users,
I'm currently working on a bundle for building lipid membranes and I have a few questions:
A part of my bundle is a lipid selector that works with AMBER-compatible pdb files. I followed the tutorial and have successfully built a selector that selects all lipids of the type I specify (say, I put in the command line 'sel POPC' then all the POPCs in the membrane get highlighted). Because of the way AMBER lipid forcefields work, individual lipids are separated into three residues, one head and two tails. I'm trying to add a function to my bundle such that individual lipids can be selected - e.g. when I select a headgroup and go [up]+[up], then the entire lipid can be selected. How can I group three residues together in a bundle?
Hi Katie, This is really a deficiency in the up/down selection hierarchy. In our Chimera program there is a "connected component" level -- which is what you want here -- that ChimeraX does not have. We have a ticket open for giving ChimeraX a fuller selection hierarchy but haven't gotten to it so far. I will add you to the recipient list for the ticket so that you will be notified when it becomes available. With your need for it, the "connected component" level should get implemented sometime this week.
Is it possible to register multiple selectors through a single function? There are many lipids that I want to include in the selector, but for now I have to copy the same function over and over if I want to do that. It will be great if I could have a list containing all the names of the lipids and have a function that registers all of them.
Yes. For bundles that register many selectors, typically they use one function that registers all the bundle's selectors when any of them are requested (rather than on a case-by-case basis). The atomic and chem_group bundles are examples. You do have to list the selectors individually in bundle_info.xml. The atomic and chem_group bundles can be found within the ChimeraX app, namely: Mac: ChimeraX.app/Contents/lib/python3.9/site-packages/chimerax Windows: <ChimeraX folder>/bin/Lib/site-packages/chimerax
Are there any built bundles that are open source? I tried to access the source code of bundles after installing them but I couldn't find the directory of which they are stored. It will be really helpful if I could refer to them.
To find where bundles from the Toolshed get installed, use the "info path" command and look for "user versioned data directory". They will be in that directory, in the "site-packages" subfolder. --Eric Eric Pettersen UCSF Computer Graphics Lab
Thank you so much for your help!
Best Regards, Katie _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
participants (3)
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Anthony James Schaefer -
Eric Pettersen -
Zeng, Katie