------ 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 .

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