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

Pavel Afonine pafonine at lbl.gov
Sat Mar 29 13:50:35 PDT 2008

On 3/29/2008 1:37 PM, Frank von Delft wrote:
>> 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.

IMHO, Yes, exactly for this purpose there must be convenience tools for 
analysis of certain parts of the whole system. But the total data base 
record should be complete and not split apart for instantaneous purpose. 
I think this could be an endless discussion which I think I'm going to 
quite now -:) Thanks all for your opinions and feedback. A few things I 
learned and will add to phenix.refine:

1) More clear message in REMARK 3 situated close by TLS records and 
explaining what is what;
2) I will add an easy to use option to phenix.pdbtools to be able to go 
back and forth between Btotal and residual components.

All these will appear in one of the next versions.

All the best and thanks again,

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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