[phenixbb] geometrical restraints between symmetry related chains
Jorge Iulek
iulek at uepg.br
Fri Dec 29 11:14:30 PST 2023
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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