Dear Edwin,
I do not know whether your question has been answered already, but the answer is simple: you have to define alternative conformations. Easiest is to generate them in coot with the “add alternate conformation” option in the right panel. You may have to delete the original unlabeled alternative conformation first though.
Alternatively, if you want to keep the original coordinates, or if the alternative residue is different: say a Leu versus a Phe you can open the pdb file with an editor and generate the alternative conformation yourself:
One of the residues gets an “A” in front of the residue name, e.g. ALEU, and the alternative residue a “B”, say BLEU. You also have to reset the occupancies to 0.5 for both conformations (or different fractions which add up to one).
Good luck!
Herman
Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Edwin Pozharski
Gesendet: Montag, 4. Februar 2019 22:35
An: [log in to unmask]
Betreff: [EXTERNAL] [ccp4bb] refmac same residue different names
Belated happy 2019, everyone.
For whatever obscure reason, I need to refine a model that has two different residue types as alternate conformers with the same residue ID. Presented with a pdb file that has such feature, Refmac fails saying this
ERROR: in chain A residue: 443
different residues have the same number
There is an error in the input coordinate file
At least one the chains has 2 residues with the same number
Check above to see error
===> Error: Problem with coordinate file
There are several ways of getting around this I can think of. Perhaps duplicate chain with strict NCS for all but the residue in question could work. Perhaps adding this residue as two separate chains and then adding enough LINK records to keep things in place could. Either solution here is inelegant and requires reformating pdb file back to sanity prior to deposition.
Is there some way to allow different geometries for alternate conformers that is native to Refmac?
Cheers,
Ed.
PS. I know that phenix.refine takes the mixed name pdb file straight up. I still want to be able to refine such structure with refmac (and buster, actually, but that's a question I already asked in the appropriate forum.
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
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