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

zhangh1 at umbc.edu zhangh1 at umbc.edu
Tue Sep 7 10:45:06 PDT 2010


Thanks Pavel!

Best Regards, Hailiang

>   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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