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
Am 13.03.2022 um 16:07 schrieb Tristan Croll:
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
Uni-Lübeck
*Universität zu Lübeck* *Institut für Biochemie*
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