I apologize if my question sounds naive or irrelevant to O. It is about reporting the structure to PDB. I've found that omitting poorly resolved side-chain atoms from refinement often improves R-free (sometimes up to 0.5%). The reason is trivial: These side chains are on a surface of protein and are naturally disordered. Because the B-factors of side and main chains are mutually restrained the refinement produces wrong B-factor values. Releasing restrains improves R_free too, but not as well as manual omitting bad side chains. It is, however, not clear, how to report such residues. >From one hand even the information about side chain based on an 'educated guess', is valuable (many analyses of the structure are not possible without a complete model). From the other hand it is kind of cheating, because B factor does not often reflect the quality of residue fitting into a density. It would be nice to have in a PDB file something similar to RS-fit R-factor of O for each residue. What people around the world do with their poorly resolved side chains? You may directly reply to my e.mail to prevent o-info from flooding. Later I'll provide a compiled report. aleshin@iastate.edu Sincerely, Alexander Aleshin
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