Hi Alex, Yes this is acceptable - symmetry-related proteins are identical and interchangeable. It can be helpful to use the PISA program (a plugin for Coot or as a webserver http://www.ebi.ac.uk/msd-srv/prot_int/cgi-bin/piserver) to identify which symmetry-related proteins are forming the biological unit, as well as what you know from biochemical studies (not to mention the position of CDRH3, etc).
The easiest way to make the change, IMHO, is to open your molecule in Coot, center on the appropriate symmetry mate, and use Extensions>Modelling>Symm Shift Reference Chain Here. -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431 On Thu, Mar 21, 2019 at 7:38 PM Liu Jingxian, Alex <ljx...@gmail.com> wrote: > Dear Colleagues, > > Recently I solved one Ab-Ag complex structure. It was indexed as p212121 > or p21212 space group and solved the structure with one Fab and one Ag in > the cell unit. The contact interface is not the one I expected (elbow > region contacts with Ag). Using symexp I got several symmetry related > molecules, showing the interface of antibody CDR with the antigen. > > > For non-structural biologist it is quite tricky to display PDB file with > symmetry related files. To make things simple, I want to solve the > structure with the biologically relevant complex in one AU, However, > changing space groups (such as P1 or P2) didn't help and I failed in the > following steps. Some people really added the symmetry related molecules > into the final pdb (merge and rename the chain ID of the mate molecules). > So is it acceptable in structure community? Many thanks. > > > Best Regards, > > Jingxian > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
