Oops! My bad - was responding on the move, and forgetting my own implementation. You're right, the "isolde restrain distances" command works on a per-residue basis, so sidechain atoms will be included regardless. On the other hand, the "isolde release distances" command works per-atom, so after the restrain command you can selectively release the sidechain restraints with:

isolde release distances #1&sideonly

From: Guido Hansen <hansen@biochem.uni-luebeck.de>
Sent: 15 March 2022 16:20
To: Tristan Croll <tic20@cam.ac.uk>
Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] ISOLDE and secondary structure restraints

Thanks for your suggestions. However, I think that when applying distance restraints using the command below also distances of mainchain atoms of secondary structure elements to nearby sidechain atoms get restrainted.

isolde restrain distances #1&(helix|strand)&backbone

  What you get when using the gui is something like that:

-- Guido

Not the hard-coded helix and beta-sheet restraints, I’m afraid. But you can get a very similar (probably better, TBH) result with something like:

isolde restrain distances #1&(helix|strand)&backbone

isolde restrain torsions #1&(helix|strand) sidechain false

The advantage of those is that (a) they’ll work a bit better when the true conformation isn’t *perfect* helix or strand, and (b) they have a lot more flexibility in terms of your ability to fine-tune their behaviour (for models fetched from the Alphafold DB, try adding the argument “adjustForConfidence true” to automatically take the pLDDT and PAE values into account).

— Tristan 

On 13 Mar 2022, at 14:42, Guido Hansen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi all,

I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess:

Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script?

Cheers,
Guido

--

PD Dr. Guido Hansen
Group Leader

Universität zu Lübeck
Institut für Biochemie

Tel +49 451 3101 3122
Fax +49 451 3101 3104
E-Mail hansen@biochem.uni-luebeck.de
www.biochem.uni-luebeck.de

Ratzeburger Allee 160
23562 Lübeck

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