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

Pavel Afonine pafonine at lbl.gov
Sat Mar 29 13:22:58 PDT 2008

Hi Frank,
Hi Frank,

> All your reasons are there for the convenience of the 
> *crystallographer*, mine are for the end user (=unsuspecting biologist) 
> -- who doesn't know TLS even exists (none of used to), never mind about 
> Hirshfeld's test and how it relates to TLS (I didn't), and certainly not 
> how run it (I still don't).

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:
- 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.

In the end what's important I believe is that the output information is 
clearly accompanied with the explanations about what it represents and 
that there are tools available from both ends (phenix, ccp4) to easily  
go from partial to total and back. The rest is the matter of personal 

Pavel V. Afonine, Ph.D.
Lawrence Berkeley National Lab, Berkeley CA, USA (http://www.lbl.gov/)
CCI: Computational Crystallography Initiative (http://cci.lbl.gov/)
PHENIX (http://phenix-online.org/)

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