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
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 BioimagingWeb : CCI.LBL.gov
On Fri, Dec 15, 2023 at 7:55 AM Jorge Iulek <[email protected]> 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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