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

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