[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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