This is exactly what phenix.refine does: it puts all together so you are
not expected to have any knowledge about magic TLS matrices in PDB file
header, about right programs to convert one into another and so on. In
contrast, if one split things apart:
Yes, but no non-crystallographer cares about the crystal -- only about
the protein *in* the crystal.
- you must know that what's in ATOM record is incomplete;
- you must know that there are TLS matrices that you have to convert to
appropriate B and add to residual ones;
- you must know that there are the programs out there to do that;
- and you must know how to use these programs too.
So, having complete record doesn't require any manipulations on the
model (and so extra knowledge) .
Imagine the situation when you got a model with partial B-factors and
another part encoded in PDB header as TLS and you want to do a
refinement in SHELXL. In this case you will need to compute the total B
to start with the correct values. In contrast, if the values are
complete, you do not need to do anything.
I can indeed not imagine a non-crystallographer using SHELXL -- for
anybody using that program, converting TLS to B is the *least* of their
worries! (With all due respect, George :) It's a very small corner
case; if people jump, it's to refmac.
phx.
