Re: sequence_to_ali command

[Shoba Ranganathan <shoba AT angis.org.au>]

Dear Michel,

I have also run into problems while trying out SEQUENCE_TO_ALI. Before
reading
the PDB file, you need to include 'SET ALIGN_CODES' with the ATOM_FILES
option.
Here's my readseq.top script that works!

# readseq.top
# Modeller script to read a PDB file and write out the sequence.
# Include MODELLER library scripts
INCLUDE
# directory with input atom files
SET ATOM_FILES_DIRECTORY = './:../atom_files'
# Structure input - PDB codes:
SET ALIGN_CODES = '1fdn', ATOM_FILES = ALIGN_CODES
READ_MODEL FILE = '1fdn.pdb'
SEQUENCE_TO_ALI
# Sequence output - PIR format
WRITE_ALIGNMENT FILE = '1fdn.pir'   

I have placed this in the examples/tutorial-all directory and it reads
the
PDB file available for the tutorials.

The output '1fdn.pir' looks like this:

>P1;1fdn
structureX:all:   1 : :  55 : :undefined:undefined:-1.00:-1.00
AYVINEACISCGACEPECPVNAISSGDDRYVIDADTCIDCGACAGVCPVDAPVQA/*

I hope this addresses your problem.

Shoba
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