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).

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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