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
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