[chimerax-users] Replacing regular residues with unusual ones

[Anthony James Schaefer]

Noor,

My SEQCROW plugin can technically do this, but Eric and Elaine's methods are probably easier for this type of thing.

You have to add the 2MR side chain to the substituent library:

  1.  Tools -> AaronTools -> Add to Personal Library
  2.  select side chain of a 2MR residue
  3.  give it a name, ignore conformer stuff (it's only used by another program)
  4.  click 'add current selection to library'

Before you do this, you might also need to set a directory for SEQCROW to store substituents. This is called 'Personal AaronTools library folder' in the 'SEQCROW' section of ChimeraX's settings. Then, chain a residue into 2MR with SEQCROW's change substituent tool:

  1.  Tools -> Structure Editing -> Change Substituents
  2.  select beta carbon on the residue
  3.  if you're worried about steric clashing, check 'relax substituent'
  4.  enter a new residue name
  5.  click 'substitute current selection'

The atoms will have the wrong names. I've been playing around with making SEQCROW aware of proximity names, so it'll automatically use CB, CG, CD, etc. If you want to try that, you can get SEQCROW from the dev branch on GitHub:
https://github.com/QChASM/SEQCROW/tree/dev

If you scroll down on that page, there's instructions on how to install it. Note that this version only works with recent daily builds of ChimeraX. You'll also have to check 'use distance labels' on the change substituents tool.

Best,

Tony


________________________________
From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of anaa2 <anaa2 at mrc-mbu.cam.ac.uk>
Sent: Tuesday, February 9, 2021 8:29 PM
To: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: [chimerax-users] Replacing regular residues with unusual ones

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


Hi,

In ChimeraX can a regular residue be replaced with an unusual one using
the swapaa function(pdb code 2MR)?

Best wishes,
Noor
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