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