Re: [modeller_usage] regarding chain identifiers ...

[Modeller Caretaker <modeller-care@ucsf.edu>]

On Wed, Apr 14, 2004 at 12:39:27AM +0530, gowthaman ramasamy wrote:
> sorry to bother u with this simple question ...
> 
> I use following top script to extract sequences from pdb file '1PFZ'.
> works fine. But it reads all the different chain (A,B,C ..etc). what
> should i do if i want to get only sequence of chain A.
> 
> read_model  FILE = '1PFZ',
> sequence_to_ali atom_files = '1PFZ', align_codes = 'gowtham'
> write_alignment file='seq.pir'
> 
> I tried the following and did not work
> read_model  FILE = '1PFZ',MODEL_SEGMENT = '@:A' 'X:A' 

The correct format should be
MODEL_SEGMENT = 'FIRST:A' 'LAST:A'
to read all residues in chain A. This was changed between 6v1 and 6v2
since '@' and 'X' sometimes clashed with actual residue names. The
current version of the online documentation should describe this
correctly:
http://salilab.org/modeller/manual/node72.html

	Ben Webb, Modeller Caretaker
-- 
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