Hi, I thank guidance from Nigel and Pavel, and as a feedback to my previous question I mention that "approach" "c" in the initial post seems to have worked nicely, with just one "shared" residue.     Best, Jorge On 12/16/23 00:25, Pavel Afonine wrote:

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 : [email protected] 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 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]