[phenixbb] reference torsion restraints for nucleic acids in real_space_refine

Oleg Sobolev osobolev at lbl.gov
Mon Oct 7 11:48:45 PDT 2019

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?


> 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:

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
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