[chimerax-users] Building ChimeraX Bundle

[Eric Pettersen]

> On Feb 1, 2022, at 10:21 AM, Zeng, Katie via ChimeraX-users <chimerax-users at 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
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