[phenixbb] geometrical restraints between symmetry related chains

[Pavel Afonine]

Hi Jorge and Nigel,

indeed, defining the bond across symmetry is trivial (using 
refinement.geometry_restraints.edits) and defining the angle is not 
implemented in Phenix. To check if the bond you defined was actually 
created and used, please inspect the .geo file that, in case of success, 
should list that bond.

As Nigel said, please feel free to reach us off list with the model file 
and we will help if needed.

All the best!
Pavel

On 12/15/23 18:15, Nigel Moriarty wrote:
> 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 <http://CCI.LBL.gov>
> ORCID : orcid.org/0000-0001-8857-9464 
> <https://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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