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 [email protected] www.bhabhaekiertlab.org

On Aug 23, 2021, at 12:22 PM, Nigel Moriarty 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 : [email protected] 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 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 [email protected] www.bhabhaekiertlab.org

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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 [email protected] www.bhabhaekiertlab.org

On Aug 23, 2021, at 8:49 PM, Pavel Afonine 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 [email protected] www.bhabhaekiertlab.org

...

On Aug 23, 2021, at 12:22 PM, Nigel Moriarty 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 : [email protected] 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 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 [email protected] www.bhabhaekiertlab.org

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