I'm trying to come to grips with the recent PDB policy for depositing files which have the TLS model expanded out into individual ANISOU records. Up until now I've been using tlsextract/tlsanl to prepare such files, but now I've just tried using the new refmac option TLSO ADDU and I'm confused.
My structure was refined using a pure TLS model. That is, all Biso terms for protein atoms were fixed at the Wilson B, and then refmac refined the TLS parameters and an overall aniso B correction. I took my previous "final" refinement run in refmac, added the TLSO ADDU keyword to the input script, and reran it. So now I have two parallel PDB files: the first one produced by refmac/tlsextract/tlsanl (no TLSO option) the second one produced by refmac (TLSO ADDU option) The BISO and ANISOU records in these are not quite the same. Not wildly different, but more than I can attribute to round-off error. Even more confusing, the water molecules in the second file have their own ANISOU records. Parvati analysis shows their descriptions are not even close to being isotropic. How/what/why did my waters get subject to aniso refinement? They are not part of any TLS group, and I didn't ask for any individual B refinement of any sort! -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
