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'
#this works but writes only a chain break and * (/*) as a third line in output file 'seq.pir' many thanks in advance .... i could not get answer from list archives. i am sorry to bother you guys.
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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gowthaman ramasamy -
Modeller Caretaker