[phenixbb] reference torsion restraints for nucleic acids in real_space_refine

[Oleg Sobolev]

Hi Daniel,


> In phenix.real_space_refine, I'm using a reference model for torsion
> restraints for a RNA/protein complex. I noticed in the log file under the
> section "Adding Reference Model Restraints (torsion)" that only the amino
> acid residues and some modified nucleotides are listed in the "Reference
> Model Matching Summary" but not the standard nucleotides. Does this mean
> that they are not restrained?

Yes.


> I checked the _initial.geo file and there are no torsion restraints for
> the standard nucleotides in the "Reference torsion angle restraints"
> section. Are they not supported by default?

They are supported. Most likely there is a large discrepancy between model
and reference and Phenix was not able to match them. What is sequence
similarity between them? Currently the threshold is 0.85. You can change it:
reference_model.search_options.chain_similarity_threshold

If you send me (off-list) the files (model, reference, ligands, no map
needed) I can take a closer look. Files will be kept confidential.

Best regards,
Oleg Sobolev.


> My workflow was this: run ready_set on the initial model and then supply
> real_space_refine with a reference model and the ready_set cif file with
> the ligands.
>
> Regards,
> Daniel
>
>
>
>
>
>
>
>
>
> När du har kontakt med oss på Uppsala universitet med e-post så innebär
> det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör
> det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
>
> E-mailing Uppsala University means that we will process your personal
> data. For more information on how this is performed, please read here:
> http://www.uu.se/en/about-uu/data-protection-policy
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20191007/eb5aeeff/attachment.htm>