FW: rationale for assigining the coordinates with a break ( | )

[Modeller Care <modeller-care@ucsf.edu>]

------ Forwarded Message
From: "Dr.Shyam Charan Mallena" <shyam AT gvkbio.com>
Reply-To: shyam AT gvkbio.com
Date: Fri, 28 Feb 2003 12:23:09 +0530
To: bozidar AT salilab.org, modeller-care@ucsf.edu
Subject: rationale for assigining the coordinates with a break ( | )

Sir,
 
{Sub : To know how or what considerations are followed to model a protein
with breaks}
 
It is a common occurance to get breaks in reference proteins "|" whis is due
to non availability of a certain number of coordinates in the reference
protein.
 
In the assigining of coordinate manually this reference is not acceptable
many a times.
 
But it works many a times with modeller (I've used Modeller from insight II
(Accelrys) at bioCampus - a subsidary of gvkBio Sciences - Hyderabad India).
 
 What is the rationale for assigining the coordinates with a break ( | ) in
reference protein in modeller.
 
 
Also how exactly is the minimization or dymanics done (If at all) in
modeller. What are the considerations for such an approach ?
 
Regarding model with a loop : In Modeller :
 
Consider the following example :
 
                    PDF Violations     Energy
 
Model 1 :       6693.9                392.083
 
Model 2 :         960.0                749.346
 
which model is prefferable to the other and the rationale.
 
thanking you,
 

                 Dr. SHYAM CHARAN MALLENA

                   

                          CALL # +91  -40  5551 9990   Ext : 149
 
             210, My Home Tycoon, Kundanbagh,

                                 Begumpet Hyderabad - 500016 .


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