[phenixbb] change sigma for an already restrained bond

[Nigel Moriarty]

Jorge

This somehow ended up in my spam. Can you send me the files off-list?

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : NWMoriarty at LBL.gov
Web  : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464


On Tue, Apr 16, 2024 at 11:33 AM Jorge Iulek <iulek at uepg.br> wrote:

> Hi,
>
>         Well, people are very busy, but maybe one starting information: is
> tightening of one single bond (through its sigma value) meant to be
> possible?
>         Thanks!
>
> Jorge
>
> On 4/12/24 16:45, Jorge Iulek wrote:
> > Dear all,
> >
> >      I would like to change the sigma value for an already restrained
> > bond.
> >      I enter for phenix.refine:
> > "
> >      bond {
> >        action = add delete *change
> >        atom_selection_1 = chain D and resid 493 and name CA
> >        atom_selection_2 = chain D and resid 493 and name CB
> >        symmetry_operation = None
> >        distance_ideal = 1.532
> >        sigma = 1.02e-2
> >        slack = None
> >        limit = -1.0
> >        top_out = False
> >      }
> >
> > "
> >
> >      In the log I get:
> >
> > "
> > ...
> >    Custom bonds:
> >      bond:
> >        atom 1: "ATOM  14355  CA  ALA D 493 .*.     C  "
> >        atom 2: "ATOM  14358  CB  ALA D 493 .*.     C  "
> >        symmetry operation: x,y,z
> >        distance_model:   1.511
> >        distance_ideal:   1.532
> >        ideal - model:    0.021
> >        slack:            0.000
> >        delta_slack:      0.021
> >        sigma:            0.0102
> >      Total number of added/changed bonds: 1
> > ...
> > "
> >
> >      But in the .geo file I read:
> >
> > "
> > User supplied restraints: 1
> > Sorted by residual:
> > bond pdb=" CA  ALA D 493 "
> >       pdb=" CB  ALA D 493 "
> >    ideal  model  delta    sigma   weight residual
> >    1.532  1.511  0.022 1.28e-02 6.10e+03 2.85e+00
> > "
> >      1.28e-02 is the default value.
> >
> >      On the other hand, sigma changes for angles and dihedrals seem to
> > work as expected (the intended values are echoed to the .geo file).
> >      To add up, if a bond is *added*, the value is in the .geo file.
> >
> >      I observe this for both
> > 1.20.1-4487
> > 1.21-5207
> >      versions.
> >
> >      So, in short, should I be allowed to *change the sigma* for a
> > specific *bond*? How should I do it?
> >      Thanks
> >
> > Jorge
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