[phenixbb] will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb?

Pavel Afonine pafonine at lbl.gov
Tue Sep 7 10:32:14 PDT 2010


  Hi Hailiang,

> I tried the following code for PDB 1SX3:
>
> *******************
> phenix.tls 1SX3.pdb combine_tls=true
> ********************
>
> but it ended up with:
>
> ***********
> ======================= TLS groups from PDB file header
> =======================
>
> Sorry: Bad TLS selection: start index>  end index.
> *******************

yes, the PDB file

http://www.pdb.org/pdb/files/1SX3.pdb

has the wrong TLS selection:

(...)

REMARK   3   TLS GROUP : 10
REMARK   3    NUMBER OF COMPONENTS GROUP : 4
REMARK   3    COMPONENTS        C SSSEQI   TO  C SSSEQI
REMARK   3    RESIDUE RANGE :   D   561        D   135

(...)

I couldn't find any documentation on  this matter, but based on my 
survey of PDB entries I found that the start_index (561 above) should be 
less than end_index (135 above), which is not the case for this TLS group.

> By the way, do I have to specify the selection or phenix.tls will
> automatically do it based on PDB header?

The TLS information is extracted from PDB file header automatically.

Pavel.

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