Looking at the PDB file of late we have examples where there are atoms missing in a number of ligands..and no easy way to clean up. Only one molecule at a time...it's a long and torturous job!
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- "Sweet"Jan 25, 2012
- The PDB sort of does what it is meant to - in many cases it's not possible to model a disordered part of a ligand into density, and so the crystallographer doesn't model it - but keeps the compound that was used as opposed to just the observed portion in the header, creating a mismatch. There are also complex cases where two conformations are observed, and the occupancy is set to 0.5 for each - recover from coords is then also difficult.
Lots of effort across the wwPDB has gone into remediation of ligand structures, and it is a lot lot better than it was!Jan 26, 2012
- Well, there is certainly not the PDB to blame (we should be happy that they collected all of it). Maybe the crystallographer do not care enough for the small molecules - at least no those who publish in PDB (I bet in industry they have a lot of excellent small molecule X-Ray data behind closed walls).Jan 26, 2012