[modeller_usage] Modeling core residues without loop regions
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Subject: [modeller_usage] Modeling core residues without loop regions
From: "Vimalkumar Velayudhan" <>
Date: Wed, 14 Jun 2006 05:05:00 +0530
Dear MODELLER users,
I was looking for answers to the following questions?
1. What is the best approach to model proteins with large insertions
(approximately 50residues) at different parts of the protein. Example
AAAAAA---------------------------------BBBBBB---------------------------------------------CCCC
Even if the alignment is good, I get an exceeded maxmolpdf error in
the model building stage. I am not sure what value to set for the
maxmolpdf .
2.Is it possible to build only the core residues without the insertions?
It would be helpful if you can point me to references related to the same.
--
Vimalkumar Velayudhan