[modeller_usage] modeling a 2 domain protein with interdomain restraints

[Michel Seigneuret <>]

Hi Modeller experts,
Here is my problem. I would like to build a model of a 2 domain
protein. I have templates for each domain as well as additional 
interdomain distance restraints from crosslinking data.
As I understand it is possible to introduce these additionnal distance 
restraints in the input file. 
However I also notice from  FAQ n°1 that in general :"...the relative 
orientation of the two domains the resulting model will probably have 
an incorrect relative orientation of the two domains ...".
So I suspect there will be a conflict between my (correct) additionnal
interdomain distance restraints and the (incorrect) interdomain distance
restraints resulting from the initial arbitrary relative orientation of the
2 templates.
How can I solve this. Is there a way to tell Modeller not to use these latter
restraints or a way to remove these at some point ?
Thank you in advance for your help.
Best regards.

Michel

Michel Seigneuret
Institut Cochin, U567-UMR8104
Département de Biologie Cellulaire
22 rue Méchain, 75014 Paris, France
Tel: 33 (0)1 40 51 64 50 
Fax: 33 (0)1 40 51 64 54