[modeller_usage] Chimeric model

[Benoit Charloteaux <charloteaux.b AT fsagx.ac.be>]

Dear Modeller users,

I want to build a model of a chimeric protein based on two distinct 
structures. I have tried as explained in the FAQ section of the manual 
(question 4), but I only get completely unfolded structures.

Is it possible to build a chimeric model with this procedure? Where does 
this problem come from?
Any possible explanation or suggestion would be greatly appreciated!

To check my procedure, I have tried the following :

I used an older prediction that worked and which is based on a single 
template structure.

Target    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
proteinA  aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa


I made a copy of the template structure file and renamed it to do as if 
there was two distinct template structures. I tried to build a kind of 
chimeric model based on these template structures as follow :

Target    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
proteinA  aaaaaaaaaaaaaaaaaaaaaaaaaaaa----------------------------------
proteinA  -------------------------aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa 

Since the two template structures used for the prediction correspond to 
the same file, the relative orientation of both structures is correct 
(the atom coordinates are the same).

The predicted 3-D model is completely unfolded too.

Sincerely,

CHARLOTEAUX Benoit
 Centre de Biophysique Moleculaire Numerique
 Faculte Universitaire des Sciences Agronomiques de Gembloux
 Passage des deportes, 2
 B-5030 Gembloux
 Belgium
Tel1:+32(0)81/62.25.32
Tel2:+32(0)81/62.25.21
Fax:+32(0)81/62.25.22
e-mail: charloteaux.b AT fsagx.ac.be
http://www.fsagx.ac.be/bp/