[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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