Dear Senthil,
This routine selects a 4 residue long loop, and builds it in an 'ab initio ' style: initially the loop segment is completely removed, than it is built from scratch.
I would suggest to build more loops (e.g. ENDING MODEL= 50 ) and select the one with the lowest Modeller energy score (you can find it in the header of the coordinate files).
best Andras
R Senthil Kumar wrote: > > Dear modeller users, > > After i am getting the initial model using modeller if any bad regions > are there(loop regions) i am using the following module for refinement. > > INCLUDE > SET SEQUENCE = 'topmodel' > SET MODEL = 'topmodel.pdb' > SET STARTING_MODEL = 1 > SET ENDING_MODEL = 2 > CALL ROUTINE = 'loop' > > SUBROUTINE ROUTINE = 'select_atoms' > PICK_ATOMS SELECTION_SEGMENT = '0:' '3:', SELECTION_STATUS ='initialize' > RETURN > END_SUBROUTINE > > Actually i want to know whether the following module does the refinement > of the loop or the loop building with some other loop.Please tell what is > the exact use of this module.Expecting for your reply. > > Yours friendly, > Senthil kumar.R