Script for setting ligand chain IDs

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Little script for comment/suggestion (and donation to ChimeraX if you find it useful). The aim is to reassign chain-IDs and residue numbers to all ligands in a reasonably systematic fashion (because these usually get quite haphazard during model building). What it does:
- for covalent ligands that aren't sugars (or consist of a single sugar residue) the chain ID is assigned to be the same as the linked chain.
- larger branched sugars get their own chain ID ({parent chain ID}glyc{index}) where the glycan attached earliest in the chain gets index 0, etc. Residue numbering starts from the stem sugar, and goes out along the bonds through the lowest-numbered oxygens first. I personally think this distinction between single and multiple-sugar sites is ridiculous, but this is what the wwPDB in their infinite wisdom have decided upon.
- for all noncovalent ligands, assigns chain IDs according to which polymeric chain is closest to the most atoms in the ligand. Renumbers (non-waters first, then waters) starting from the next multiple of 1000 beyond the end of the polymeric chain (or the following 1000 if the gap between the last residue and the starting number is equal to or less than 100).
- any unbound ligands that are too far from the macromolecule to be captured in the first distance test (`find_close_points()` with a 5A cutoff) get a second chance - checked again against everything that's been assigned, this time with an 8A cutoff. If there are still unassigned residues, they get a chain ID of 'UNK' and a warning goes to the log.

It *appears* to work correctly in my tests (on the same system as in #4176 - 4974 protein residues, 814 ligands, two O-linked glycans, it takes about 1.3 seconds). Any comments or suggestions welcome!

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> alias st isolde step $*

> alias aw isolde add water $*

> alias awsf isolde add water sim false

> alias al isolde add ligand $*

> alias so setattr sel atoms occupancy $*

UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




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File attachment: ligand_utils.py

ligand_utils.py​

[Tristan Croll]

Added by email2trac

[Eric Pettersen]

This seems like it would fit right into the ChimeraX Recipes wiki, along with an announcement on chimerax-users...

[Tom Goddard]

Interesting. I don't understand the use case. I guess it is for people building and refining structures when they start with a PDB model with hard to use chain id assignments. I think the most important thing missing here is an explanation to tell a person why they would want to use this.

Then there is the question of what you want to do with it. It would be fine to put on ChimeraX Recipes -- I can give you write access to that GitHub repository and you can do that. I was thinking of recipes as simple stuff and this is pretty complex, but it is fine. But not sure it would reach many users. Maybe its own toolshed bundle that provides a command? Could even be a new ChimeraX command if you thought it worthwhile, although that would need good quality control, support, documentation.

[Tristan Croll]

Hmm... when you put it that way, perhaps it is a more ISOLDE-specific thing. It's a problem that generally only crops up when actively building a model starting from a somewhat-incomplete state - due to all the twists and turns, in a complex model the chain assignments and numbering can end up really scattered. Probably too small to turn into its own bundle.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 27 January 2021 22:28
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4177: Script for setting ligand chain IDs

#4177: Script for setting ligand chain IDs
----------------------------------------+-------------------------
          Reporter:  Tristan Croll      |      Owner:  Tom Goddard
              Type:  enhancement        |     Status:  assigned
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+-------------------------

Comment (by Tom Goddard):

 Interesting.  I don't understand the use case.  I guess it is for people
 building and refining structures when they start with a PDB model with
 hard to use chain id assignments.  I think the most important thing
 missing here is an explanation to tell a person why they would want to use
 this.

 Then there is the question of what you want to do with it.  It would be
 fine to put on ChimeraX Recipes -- I can give you write access to that
 GitHub repository and you can do that.  I was thinking of recipes as
 simple stuff and this is pretty complex, but it is fine.  But not sure it
 would reach many users.  Maybe its own toolshed bundle that provides a
 command?  Could even be a new ChimeraX command if you thought it
 worthwhile, although that would need good quality control, support,
 documentation.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4177#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
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