Hi I had been think of asking a friend to write a short python script that could list all residues or even all atoms (below a user defined B factor threshold) in a phenix selection format. Then I could run this and just cut and paste the residues with ADPs below 5, or 10 or 20, and run phenix.refine with anisotropic for these differing selections. The trick s getting someone to spend the hour or two I need. Any takers? :-D Mark On Aug 19, 2008, at 6:05 PM, Pavel Afonine wrote:
Hi Mark,
After refinement with TLS how should we switch to refinement with aniso individual ADPs. i know that both cannot be done simultaneously at present.
Just turn off the TLS refinement option. Since input PDB file will contain atoms with ANISOU records they will be refined as anisotropic automatically. Alternatively, you can specify which atoms to refine as isotropic or anisotropic.
Following up on Mark's question: we also have a set of structures of resolution 1.5 to 1.24 Å resolution that are good candidates for anisotropic refinement, but selecting the subset of residues to refine is not easy (for us).
We can exclude loops and terminii with high isotropic ADPs, but even for the remaining well ordered parts of the protein we are left with surface residues with well ordered main chain but less well ordered side chains (e.g, Lys and Glu), which need to be refined isotropically. Also, we would like to exclude residues with alternative conformations from anisotropic refinment.
At present its a fair amount of work to build up a residue selection to satisfy these requirements.
The goal is to make refinement completely automated where you hit Enter and get refined structure. What you describe above is one of the items in to-do list for further automation.
Also, I do not think you need to refine as isotropic the atoms with large B-factors. Yes, ac should probably be refined as isotropic. This is something to systematically study (as part of the overall planned automation).
For the moment, I would just remove from anisotropic refinement some very obvious parts that should be refined as isotropic and I'm almost sure it will be enough in most of the cases.
Pavel.
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