[phenixbb] phenix.model_vs_data TLS and ANISOU records questions

Pavel Afonine pafonine at lbl.gov
Fri Apr 1 12:28:18 PDT 2011


Hi Hailiang,

phenix.model_vs_data handles input TLS exactly as described in the paper 
you mentioned below - I didn't change anything in the relevant code 
since publication of that paper.

Essentially, there may be three types of input files:
- containing total ADP, and
- containing residual (or local or atom) ADP,
- various weird mixtures of two above,

so without trusting too much input REMARK 3 records, 
phenix.model_vs_data tries both possibilities and picks the one that 
yields a lower R-factor, which makes the program a bit slower but way 
more robust.

Pavel.

> In phenix.model_vs_data, a special handling of ANISOU records and TLS
> parameters were mentioned in
> "http://scripts.iucr.org/cgi-bin/paper?he5476". My understanding is the
> following and pls let me know if I am wrong:
>
> ************
> (1) In TLS, some programs output a PDB with ANISOU including only TLS
> B-factor (case A), and other programs output a PDB with ANISOU including
> both TLS and residual B-factor (case B).
>
> (2) In the former case (A), the ANISOU B will be added to the residual B;
> The later case (B) is straightforward. (Both will be tried and lowest
> R/Rfree will be used)
>
> (3) In the former case (A), if ATOM B records contain both TLS (isotropic
> conversion) and residual B, TLS-isotropic B will be substracted from ATOM
> B records. The later case (B) is straightforward. (Both will be tried and
> lowest R/Rfree will be used)
>
> *************
>
> Pls let me know if I am wrong somewhere. Thanks a lot!
>
> Best Regards, Hailiang
>
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