Re: [phenixbb] Peptide bond to symmetry related molecule

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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]