On Mon, Nov 15, 2004 at 02:48:46PM +1000, Praveen Madala wrote: > I have been trying to MODEL a protein with distance restraints > using MODELER version-12 with InsightII . Here I am attaching my .rsr > file, and the below are the problems i got in my trials....
You will have to ask Accelrys about InsightII. It's not our program, and the packaged version of Modeller is very very old. I recommend that you try your problem with the latest Modeller release.
> R 3 1 1 21 2 2 0 6.00000 0.3387 N:117 N:292 > R 3 1 1 27 2 2 0 8.00000 0.3387 CB:117 CG:208 > R 3 1 1 27 2 2 0 10.0000 0.3387 CB:117 CG:208 > R 3 1 1 27 2 2 0 8.00000 0.3387 CB:117 CG:211 > R 3 1 1 27 2 2 0 10.0000 0.3387 CB:117 CG:211 ... > and also I didnt under stand when to use 21, 22, 27 and 30 in > distance restraints.
That simply specifies which group to report the energy and violations in. See table 2.4 in the Modeller manual, at http://salilab.org/modeller/7v7/manual/node100.html#28305
In the latest version of Modeller, groups 21, 22, 27 and 30 correspond to:
21 X lower bound distance restraints 22 X upper bound distance restraints 27 Distance restraints 5 (X-Y) 30 Minimal distance restraints
Ben Webb, Modeller Caretaker