Using a model file as one of the templates (fwd)

[sasson iris <>]

Hi,

I send this question again because i got no reply.

I want to create a model using modeller from a group of alignmnets and 
models. Since modeller (if i understand correctly) uses only alignments 
and no models (pdb format), i would like to create alignmnets from the 
models i have, and give the alignment as one of the alignmnets in the 
multiple alignmnet given as input to modeller. However, i have no idea how 
to do this since i do not know what modeller actually does. 
An alignment that may be created from a model i already have 
 is of identical sequences of query and template like this:

>P1;str
structure :  str  :  : :  : : : : :
EFSVCGGRLIKLSHNSNSTKTSMNVNIYLPKHYYAQDFPRNKRIPTVFYLSGLTCTPDNASEKAFWQFQADKYGFAIVFP
EHLKPELLLEAVKATSWQDYVEIKKVHGFDHSYYFVSTFVPEHAEFHARNLGLI*

>P1;query
sequence :  query  :  : :  : : : : :
EFSVCGGRLIKLSHNSNSTKTSMNVNIYLPKHYYAQDFPRNKRIPTVFYLSGLTCTPDNASEKAFWQFQADKYGFAIVFP
EHLKPELLLEAVKATSWQDYVEIKKVHGFDHSYYFVSTFVPEHAEFHARNLGLI*   

and i have the model which is the str.pdb file.
I do not want modeller to put higher weight to this alignment than to the 
others (which are to real templates). The sequence identity may yield this 
result. How can i solve this?
Or if i ask it differently, what weight does modeller give to such 
alignmnets? How can i change the sequence similarity to yield the required 
result?
I will be happy to check any suggestion you may have.

Thanks,
Iris.



---------- Forwarded message ----------
Date: Sun, 6 Jul 2003 15:37:31 +0300 (IDT)
From: sasson iris <>
To: Modeller Care <>
Cc: 
Subject: Using a model file as one of the templates 


Hi,

I want to use models as well as templates to build a new model using 
modeller. That is, I have a few models that were not created by using an 
alignment and some alignments.
How can i make modeller use all of which to build a new model?

Thanks,
Iris.