[modeller_usage] Simple and Multiple Alignment

[Hugo Brandão Uchôa <>]

Dear Sir,
I´m trying to perform two kinds of modelings: one with
simple alignment (using one template) and another with
multiple alignment (using 2 templates).
However there is a problem in alignment step. I 've
use d the follow file to perform alignment with 1
template:

READ_MODEL FILE = '1hcl.pdb'
SEQUENCE_TO_ALI ALIGN_CODES = '1hcl'
READ_ALIGNMENT FILE = 'cdk10.seq', ALIGN_CODES =
'cdk10', ADD_SEQUENCE = ON
ALIGN2D
WRITE_ALIGNMENT FILE='1hcl-cdk10.ali',
ALIGNMENT_FORMAT = 'PIR'
WRITE_ALIGNMENT FILE='1hcl-cdk10.pap',
ALIGNMENT_FORMAT = 'PAP'

Modeller performs the alignment with this file, but
the result in PIR format is a file that contais just a
piece of the sequence of template:

structureX:1hcl*:   1 : :  81 :
:undefined:undefined:-1.00:-1.00
MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRTEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLV
FE*


Is there some error in the top file???

I also need a example of a top file to perform a
alignment with 2 templates.

Could somebody help me???

Thank you.

Hugo Brandão Uchôa
São Paulo State University

______________________________________________________________________

Yahoo! GeoCities: a maneira mais fácil de criar seu web site grátis!
http://br.geocities.yahoo.com/