[phenixbb] PDB deposition of tls refined structure

Paul D. Adams PDAdams at lbl.gov
Thu Nov 1 15:58:26 PDT 2007

Hi Rene,

   this is something that we are trying to address with the PDB  
deposition people. For the moment you could take out the ANISOU  
records (although this is nothing that says that you need to have  
high resolution data to deposit a structure with ANISOU records).  
That way you would still have the TLS records and the IsoB  
equivalent. Note that this is different from REFMAC which keeps the  
residual B in the B-factor column. If you explain this to the PDB I  
hope that they will understand the situation.


On Oct 30, 2007, at 7:15 AM, Rene Jorgensen wrote:

> Dear phenix users,
> I am about to deposit a 2.5A structure at the PDB. The structure has
> been refined using phenix.refine with strategy=tls+individual_sites
> +individual_adp, which actually works very well but (because of the
> tls refinement) also results in the output of ANISOU records for the
> atoms in the PDB file. When using PDB_extract during the PDB
> submission process the ANISOU record is picked up as regular
> anisotropic refinement although the resolution is too low for that.
> Should I just accept it and leave it as it is or should I correct the
> info in the Auto Dep Input Tool (ADIT) to isotropic with just the
> regular b-factor values?
> Thanks in advance,
> Rene Jorgensen
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Paul Adams
Senior Scientist, Physical Biosciences Division, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Head, Berkeley Center for Structural Biology
Deputy Principal Investigator, Berkeley Structural Genomics Center

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