[phenixbb] geometrical restraints between symmetry related chains

[Nigel Moriarty]

Jorge

It is not possible to specify a symmetry related angle in an
unambiguous fashion. Using the bond edit should give a result. If you send
the model directly to me and Pavel Afonine (not the list) we will take a
closer look.

NB. Any files sent to me will be held in strictest confidence.

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 Fri, Dec 15, 2023 at 7:55 AM Jorge Iulek <iulek at uepg.br> wrote:

> Dear all,
>
>         I am working currently on a structure that should be "peptide
> bond"
> between chains, but the "second" part of the chain is in a symmetry
> related peer. Numbering is continuous and there are justifications to
> why the chains are separately named with different chain ID's. By the
> way, this "connection" is "full of glycines" so a kind of flexible, but
> a continuous stretch can be seen at "reasonable" density (and despite
> low resolution).
>         To better explain, say I have chain C residue x to be bound to
> chain K,
> at symm operation -x-1,y-1/2,-z-1/2, residue x + 1.
>         I would prefer to really refine the presence of these "connecting"
> glycines, of course with due geometrical restraints imposed (precious at
> this low resolution).
>         phenix.refine offers:
>
> refinement.geometry_restraints.edits
>
> at
>
> bond
>
> with the possibility to indicate the
>
> symmetry_operation
>
>         for the "second atom" within the bond. But this
> "symmetry_operation"
> indication is not available (?) for the other geometry_restraints edits,
> like  angle, dihedral, etc. (eventually, planarity might also make
> easier). Do I miss anything here?
>         Currently, I see 3 possibilities:
> a) somehow (how?) I can add angle, dihedral restraints in involving
> chains in symmetry related operations
> b) I bring the symmetry related chain to its non "symmetry related"
> position and change chains names/residues ID, etc., so I go into this
> go/return of naming at each step of the refinement work/analysis
> c) I add "extra" ( + - like alternate conformation residues) residues to
> each end of the connection, such that these extra residues will receive
> due conventional geometrical restraints (as phenix.refine does for
> contiguous residues in a chain) but I force them to be on the same
> position (and probably declare 0.5 occupancy for these overlying residues).
>         "a" should be the easiest, if available somehow; "b" would be
> cumbersome during the refinement/analysis process; "c" seems to be the
> most complex but maybe the best if it works. Nevertheless, someone might
> have an easier suggestion.
>         Thanks,
>
> Jorge
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