[phenixbb] Rant: B vs TLS, anisou, and PDB headers

Frank von Delft frank.vondelft at sgc.ox.ac.uk
Sat Mar 29 13:37:42 PDT 2008

> 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.


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