[phenixbb] Secondary structure restraints

Oleg Sobolev osobolev at lbl.gov
Wed Nov 20 13:08:37 PST 2019

Hi Luca,

When you select a base pair or stacking pair in Selection Editor, find
checkbox "Enabled" on the left side. Uncheck it. Note that you can select
all base pairs and uncheck it once. Do the same for stacking pairs. This
will disable each annotation.

Another way:
Refinement settings tab -> All parameters -> Search parameters, enter
"nucleic_acid". Locate 3 "Enabled" checkboxes and uncheck them. This will
turn off nucleic acids SS restraints even if they are present in .eff file
(no need to delete/disable them).

For completeness, command-line argument to do this is
"nucleic_acid.enabled=False". If it is True (default) and there is no
nucleic acid SS annotations (you deleted all of them), Phenix will try to
find them before refinement. This is what you observed.

To make sure you did not have nucleic acid SS restraints in refinement,
locate something like:
395 hydrogen bonds defined for protein.
    1135 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.35
in the log-file.

Best regards,
Oleg Sobolev.

On Wed, Nov 20, 2019 at 11:51 AM Luca Pellegrini <lp212 at cam.ac.uk> wrote:

> I have a protein-DNA complex and would like to apply SS restraints. What
> is the best way to apply the SS restraints to the protein only, using the
> GUI? I have tried the following:
> Select ‘Use secondary structure restraints’ in the ‘Refinement Settings’
> tab
> ‘Select Atoms’
> In the Selection Editor window, 'Find Secondary Structures'
> Removed manually all nucleic acid restraints in ‘Base Pairs’ and Stacking
> Pairs’ tabs
> Save and close.
> However, phenix refinement keeps switching SS restraints for nucleic acids
> to True.
> Kind regards,
> Luca
> Luca Pellegrini, PhD
> Department of Biochemistry
> University of Cambridge
> Cambridge CB2 1GA
> United Kingdom
> lp212 at cam.ac.uk
> tel.: 0044 1223 760469
> https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group
> @PellegriniLab
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