[modeller_usage] Problem modelling protein dimer close to DNA ...
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Subject: [modeller_usage] Problem modelling protein dimer close to DNA ...
From: Sergio Garay <>
Date: Fri, 21 Jan 2011 07:11:55 -0500
Dear Modeller's Users:
I'm trying to model a protein dimer interacting with a small DNA molecule. Following the manual instructions I was able to build my dimer using:
>P1; my_target xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx --> first monomer
/ yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy --> second monomer * >P1; my_template hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh --> first monomer / kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk ---> second monomer
*
But I have some problems to add my DNA molecule as an additional restraint:
I added to my script:
env.io.hetatm = True
And I also added my DNA molecule (all the DNA atoms were named HETATM) into the template pdb and modified my alignment in this way:
>P1; my_target
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx --> first monomer
---------- --> alignment of extra dna residues (I'm not sure is this is right) /
yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy --> second monomer
---------- --> alignment of extra dna residues (I'm not sure is this is right) *
>P1; my_template
hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh --> first monomer
---------- --> alignment of extra dna residues (I'm not sure is this is right) /
kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk ---> second monomer ---------- --->alignment of extra dna residues (I'm not sure is this is right)
/ ---------------------------------------------------- ---> 1st strand of DNA ............. / ---------------------------------------------------- ---> 2nd strand of DNA
.............
* Modeller worked without any warning but my dimer pass through the DNA molecule, so this is not working.
Any help would be very appreciated.
Sergio
-- Sergio Garay Dr. en Ciencias Biológicas
Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221