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 ======================================================================= Shoba Ranganathan, Ph D Tel:+61-2-9351-1870 AGIC/ANGIS, Bay 16, Suite 104 Toll free:1-800-728-028 Australian Technology Park Fax:+61-2-9351-1878 Eveleigh NSW 1430 Australia Personal URL: http://seal.angis.org.au/~shoba ================MolMod Home Page: http://molmod.angis.org.au===========