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

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 sassonir@cs.bgu.ac.il To: Modeller Care modeller-care@salilab.org Cc: modeller_usage@salilab.org 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.