[phenixbb] geometrical restraints between symmetry related chains

[Jorge Iulek]

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 : 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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