[chimerax-users] ISOLDE and secondary structure restraints

[Guido Hansen]

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 at 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*
>>
>> Tel +49 451 3101 3122
>> Fax +49 451 3101 3104
>> E-Mail hansen at biochem.uni-luebeck.de
>> www.biochem.uni-luebeck.de
>>
>> Ratzeburger Allee 160
>> 23562 Lübeck
>>
>> _______________________________________________
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-- 
Re: email signature
*PD Dr. Guido Hansen*
Group Leader

Uni-Lübeck

*Universität zu Lübeck*
*Institut für Biochemie*

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

Ratzeburger Allee 160
23562 Lübeck
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