[buster-discuss] Occupancy refinement w/o residual repulsion
Young-Jin Cho
yjcho at brandeis.edu
Mon Feb 8 16:14:31 CET 2010
Dear Buster users,
I am new to Buster and want to run occupancy refinement while avoiding residual repulsion issues. If anyone is good at this kind of refinement, could you give me some tips?
For example, I built 3 different ligands (among 2 are coupled each and the other, so basically 2 kinds of alternative ligands need to be defined while one of which has two molecules in one ligand group).
I edited my model with A and B alternative ligands followed by their chemical names under the same chain name (FYI. at first, I put all them different chain names but didn't go through). Unfortunately, this method didn't let refinement proceeds. The followings are part of error message (still I didn't do anything like commanding occupancy run but just tried how it goes. I wish I need to get how I can apply this method as well).
>>> pdbchk >>> different residue name - see below
>>> pdbchk >>> HETATM 7937 O2ABADP C 1 -12.774 0.417 19.550 0.70 15.23 O
>>> pdbchk >>> HETATM 7968 O3PAAMP C 1 -12.711 2.906 19.482 0.30 18.81 O
>>> pdbchk >>> HETATM 7968 O3PAAMP C 1 -12.711 2.906 19.482 0.30 18.81 O
>>> pdbchk >>> HETATM 7995 O3 APO3 C 1 -15.097 0.357 16.092 0.30 19.89 O
With many thanks in advance,
Young-Jin Cho
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