[modeller_usage] Help needed concerning the alignment file

[doppelt olivia <>]

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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