Dears, we have an unexplained problem when using the SEQUENCE_TO_ALI command: only the first residue of the MODEL (template) file is transfered to the alignment array, e.g if we write an alignment file, only the first residue appears, though the right number of residues is written by the program (the second line of the alignment file includes the first and last residue number of my pdb file). Here is an example of the output i get when try to test this command on 5fd1:
>P1;all structureX:all: 1 : : 106 : :undefined:undefined:-1.00:-1.00 A*
I would like to precise that we get this problem when using the example loop routine, as well as when simply testing the command e.g: READ_MODEL FILE = '5fd1.ent' SEQUENCE_TO_ALI WRITE_ALIGNMENT FILE='5fd1.ali'
What did we do wrong?
Regards.
Michel Giorgi Lab. Cristallochimie Fac. St. Jerome, Marseille, France
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===========
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Shoba Ranganathan