[phenixbb] Peptide bond to symmetry related molecule

Damian Ekiert damian.ekiert at ekiertlab.org
Mon Aug 23 19:36:51 PDT 2021


Thanks Nigel and Pavel for your help with this. In case it is helpful to someone else down the road, the summary is:

Generic bonds can be specified to a symmetry mate by editing the geometry_restraints.edits section of your .eff file. This will create a bond length restraint between any two atoms of interest, but restraining the angles, torsions, etc. is not currently possible. An example of how to specify such a bond is below:

refinement.geometry_restraints.edits {
  n_44_selection = chain A and resname ASP and resid 44 and name N
  c_215_selection = chain A and resname VAL and resid 215 and name C
  bond {
    action = *add
    atom_selection_1 = $n_44_selection
    atom_selection_2 = $c_215_selection
    symmetry_operation = -x-1,-x+y-1,-z-1/3
    distance_ideal = 1.335
    sigma = 0.02
    slack = None
  }
}

Best,

Damian

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Damian Ekiert
Assistant Professor
Skirball Institute | NYU School of Medicine
Depts. Cell Biology and Microbiology
damian.ekiert at ekiertlab.org
www.bhabhaekiertlab.org

> On Aug 23, 2021, at 8:49 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
> 
> Hi Damian,
> 
> 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.
> 
> Pavel
> 
> 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
>> 
>> Best,
>> 
>> Damian
>> 
>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> Damian Ekiert
>> Assistant Professor
>> Skirball Institute | NYU School of Medicine
>> Depts. Cell Biology and Microbiology
>> damian.ekiert at ekiertlab.org
>> www.bhabhaekiertlab.org
>> 
>> 
>> 
>>> On Aug 23, 2021, at 12:22 PM, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:
>>> 
>>> Damian
>>> 
>>> 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.
>>> 
>>> Cheers
>>> 
>>> Nigel
>>> 
>>> ---
>>> 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!
>>> 
>>> Best,
>>> 
>>> Damian
>>> 
>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>>> Damian Ekiert
>>> Assistant Professor
>>> Skirball Institute | NYU School of Medicine
>>> Depts. Cell Biology and Microbiology
>>> damian.ekiert at ekiertlab.org
>>> www.bhabhaekiertlab.org
>>> 
>>> 
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