Just for anyone's reference, adding a occ.params file with the following content, refinement { refine { occupancies { constrained_group { selection = chain A and (resseq 74 or resseq 401 or resseq 402) and altloc A selection = chain A and (resseq 74 or resseq 401 or resseq 402) and altloc B } } } } (where 401 and 402 are the NAGs and 74 the Asn they're conjugating) was what I was looking for. 2014-06-14 21:46 GMT+02:00 Benjamin Stauch :

Hi Pavel,

many thanks, and great guess - there is indeed a TER between two conformers. I imagine deleting this will solve my problem. As for my second question, probably I would need to do something along the lines of example #4 in your link and define a constrained_group?

Thanks!

Ben

2014-06-14 21:36 GMT+02:00 Pavel Afonine :

Hi Ben,

...

I do a refinement of a glycoprotein that has a NAG-NAG attached to an

...

Asn. The data set is very high resolution and I am positive there is indication of a secondary conformation of the entire attachement. I modeled a second conformation in Coot and run my refinement, with the "adjust occupancy" option checked. After initially setting both occupancies to 0.5, I am puzzled to see one of the NAGs to be refined to 0.45 (conformer A) and 0.75 (conformer B) occupancy .. For the other NAG, and indeed all amino acid residues, things always add up like they should.

Additionally to this, I was wondering if there was an easy option to restrain each conformer of the entire Asn-NAG-NAG group to have uniform occupancies -- i.e. the Asn and both NAGs of conformer A to have identical occupancy.

I'm pretty sure the problem stems from incorrectly formatted PDB file (perhaps TER records inserted between conformations/residue, etc..). If you send me PDB file or just a fraction of it with residues/ligands in question I will tell what exactly is the root of the problem.

More information about how phenix.refine does occupancy refinement: http://phenix-online.org/documentation/reference/ refinement.html#occupancy-refinement

Pavel