Lazy body's solution - read the PDB into pisa, and output the "assembly" .
This will a) move multiple molecule copies in an asymmetric unit to symmetry versions which make the best biological sense, and
                b) if necessary add extra symmetry mates to make up an assembly.

Example Heamoglobin in P41212 - This has one A chain and one B chain in the asymmetric unit, but the tetramer is generated by a two-fold symmetry operator producing another copy of A & B
Eleanor

On Fri, 22 Mar 2019 at 08:23, <[log in to unmask]> wrote:

Hi Alex,

 

Kevin is right. To clarify things a little, you don’t have to use the symmetry mate selected by the molrep program. You can take the symmetry mate that makes the relevant biological interactions instead. No need to change the space group.

 

You have to delete the molecule that does not make the relevant contacts and add the symmetry mate of this molecule that does make the relevant contacts and maybe run one more cycle of refinement to get rid of rounding errors. (and make sure that the procedure you used is correct)

 

Best,

Herman

 

Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Kevin Jude
Gesendet: Freitag, 22. März 2019 04:11
An: [log in to unmask]
Betreff: [EXTERNAL] Re: [ccp4bb] crystal contacts and biologically relevant contacts

 

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

 

 

On Thu, Mar 21, 2019 at 7:38 PM Liu Jingxian, Alex <[log in to unmask]> 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

 

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