------ Forwarded Message From: "Dr.Shyam Charan Mallena" shyam@gvkbio.com Reply-To: shyam@gvkbio.com Date: Fri, 28 Feb 2003 12:23:09 +0530 To: bozidar@salilab.org, modeller-care@salilab.org 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 .
------ End of Forwarded Message
