Regarding Modeller model building script
Dear Modellers & Respected Sir Benn, If i am correct Modeller uses distance restraints from multiple templates based on alignment, Tell me the way to use one complete template during modeling and chunks from others. I tried doing that but GDT score decreased when i aligned chunks to one complete template alignment. The aligned chunks were covering target region which was unaligned by one selected complete template span. So HOW TO GENERATE FOLD BASED ALIGNMENT WHICH IMPROVES GDT SCORES BY INCREASING CONSIDERATION WEIGHT OF A SINGLE TEMPLATE AS COMPARED TO OTHERS IN MODELLING.
Thanks Ashish
Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA
On 6/30/11 11:44 PM, Ashish Runthala wrote: > If i am correct Modeller uses distance restraints from multiple > templates based on alignment
Yes, and also other restraints that take the alignment into consideration, such as dihedral restraints.
> Tell me the way to use one complete template during modeling and > chunks from others.
The information from multiple templates is weighted automatically by several factors, including the local similarity between template and model sequence. See the Modeller 1993 JMB paper for details. To have Modeller use one template in preference to another, modify your alignment such that that template is aligned and the other is not. If both templates are aligned, you cannot manually set the weighting.
Ben Webb, Modeller Caretaker
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Ashish Runthala -
Modeller Caretaker