[phenixbb] Peptide bond to symmetry related molecule
pafonine at lbl.gov
Mon Aug 23 17:49:53 PDT 2021
it is possible to define bond between symmetry related atoms. In this
case it won't be made automatically, so you need to make a parameter
file for that.
On 8/23/21 10:04, Damian Ekiert wrote:
> Hi Nigel,
> I hadn’t checked, but had a look now and I am only finding records that start with “nonbonded” (examples pasted below for the two connections that I would like to make). If you don’t mind having a look, I will send you some files on the side. Thanks!
> nonbonded pdb=" N LEU B 1 "
> pdb=" C PRO B 12 "
> model vdw sym.op.
> 3.003 3.350 -x-1,-x+y,-z-1/3
> nonbonded pdb=" N ASP A 44 "
> pdb=" C VAL A 215 "
> model vdw sym.op.
> 1.560 3.350 -x-1,-x+y-1,-z-1/3
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Damian Ekiert
> Assistant Professor
> Skirball Institute | NYU School of Medicine
> Depts. Cell Biology and Microbiology
> damian.ekiert at ekiertlab.org
>> On Aug 23, 2021, at 12:22 PM, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:
>> Peptide bonds are usually automatic, however, because only bond restraints are permitted across symmetry mates it can sometimes be "interesting". Have you try refining and checking the .geo file for the bond restraints?
>> Please feel free to send the model file directly to me for testing purposes.
>> Nigel W. Moriarty
>> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
>> Lawrence Berkeley National Laboratory
>> Berkeley, CA 94720-8235
>> Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
>> Fax : 510-486-5909 Web : CCI.LBL.gov
>> ORCID : orcid.org/0000-0001-8857-9464
>> On Mon, Aug 23, 2021 at 7:19 AM Damian Ekiert <damian.ekiert at ekiertlab.org> wrote:
>> Hi All,
>> We are refining several structures in which the N-terminal residue of chain A appears to form a peptide bond to the C-terminal residue of its symmetry mate, chain A. In reality, the target protein consists of 4 identical helical repeats that pack end to end. Slippage and averaging over the 4 possible registers leads to the appearance of an infinitely long polymer in the crystal, with no breaks between protomers.
>> Is it possible to enforce a peptide bond to symmetry mates in Phenix, and what is the easiest way to do this? I have found a several cases in the archives on how to deal with symmetry clashes, but struggling to figure out how to deal with a peptide bond.
>> Thanks for your help!
>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> Damian Ekiert
>> Assistant Professor
>> Skirball Institute | NYU School of Medicine
>> Depts. Cell Biology and Microbiology
>> damian.ekiert at ekiertlab.org
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