id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
3138	Build out full side-chains for MD simulations	tic20@…	Eric Pettersen	"Tristan wants to be able to add atoms to make complete side-chains (all heavy atoms plus hydrogens) matching OpenMM templates.

Begin forwarded message:

From: Tristan Croll 
Subject: Re: ISOLDE and ChimeraX plan for the future
Date: May 4, 2020 at 3:24:17 PM PDT
To: Tom Goddard 

Hi Tom,

Coming back to your question on things from the ChimeraX end that I think could help ISOLDE. I can think of a few - some quite easy, some a little more complex.

On the easy side (but moderately urgent): correcting residues where the hydrogens don't match the MD template. I actually have a lot of the necessary infrastructure in place - in particular a method to ""complete"" a residue with missing atoms (and rename wrongly-named ones), based on graph matching to its CCD template using NetworkX. Problem with that is that (a) it currently adds *all* atoms in the template, including superfluous acid/phosphate hydrogens and atoms that should be removed due to covalent bonding; and (b) it doesn't add hydrogens that are missing from the template but should be there for MD. It should be quite straightforward to use the same graph matching approach to the MD residue template to decide which atoms to remove, but adding the missing hydrogens is more difficult because the MD template has no explicit geometry information. It seems certain that everything necessary for that could be found in Eric's AddH code, but I haven't come to terms with that enough to figure out how.

That one alone could make a pretty huge difference - while ISOLDE has a library of about 15,000 residues, a single-hydrogen mismatch currently just triggers an ""isolde doesn't recognise this residue"" message, which isn't particularly helpful in fixing it. In fact, right now it doesn't even tell the user if there *is* a paramterisation for that residue but the atoms don't match... needs work. Having a ""this residue looks like XXX but it has an extra ... / is missing ... Would you like to fix it?"" message instead would immediately boost usability.

..."	enhancement	closed	moderate		Structure Editing		fixed		Tom Goddard				all	ChimeraX