Hello,
I've been trying to use Modeller on an alignement file obtained from a clustalw use. I have the pdb file in the same repertory.
I used a script, that i found in the examples files of Modeller.
When I try to use Modeller, the following error is made : rdpir___648E> Alignment sequence not found in PDB file: 1 ./1tu7.pdb
Here is my scipt :
#! /usr/bin/env python
from modeller.automodel import * import sys
env = environ() ali = sys.argv[1] pdb = sys.argv[2] nb = int(sys.argv[3])
env.io.atom_files_directory = pdb
a = automodel(env, alnfile=ali, knowns='1tu7', sequence='13gs')
a.starting_model = 1 a.ending_model = nb a.make()
Here is my alignment file 13gs-1tu7.ali:
>P1;1tu7 structureX:1tu7: ::: ::: 0.00: 0.00 MS-YKLTYFSIRGLAEPIRLFLVDQDIKFIDDRIAKDDFS--SIKSQFQFGQLPCLYDGD QQIVQSGAILRHLARKYNLNGENEMETTYIDMFCEGVRDLHVKYTRMIYMAYETEKDPYI KSILPGELAKFEKLLATRGNGRNLILGDKISYADYALFEELDVHQILDPHCLDKFPLLKV FHQRMKDRPKLKEYCEKRDAAKVPVNGNGKQ*
>P1;13gs sequence:13gs: : : : ::: 0.00: 0.00 MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASCLYGQLPKFQDGD LTLYQSNTILRHLGRTLGLYGKDQQEAALVDMVNDGVEDLRCKYISLIYTNYEAGKDDYV K-ALPGQLKPFETLLSQNQGGKTFIVGDQISFADYNLLDLLLIHEVLAPGCLDAFPLLSA YVGRLSARPKLKAFLASPEYVNLPINGNGKQ*
the pdb file 1tu7.pdb is in the same directory.
I changed a lot of things in the script or in the alignment file, it doesn't change anything.
Any help would be good, Thanks in advance,
Olivia Doppelt
___________________________________________________________________________ Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international. Téléchargez sur http://fr.messenger.yahoo.com