Dear modellers,
I have searched the archives of the discussion forum for this and found a few questions, but no answers. I wish to impart the template structure to a sequence exactly, and select only the loops for refinement. I am using modeller 7v7, and have not switched to 8 yet. I would be interested in ways to do this for both versions, but most interested in 7v7. Currently, I use a snippet of top script taken from one of the examples that looks like this:
SUBROUTINE ROUTINE = 'select_atoms' PICK_ATOMS SELECTION_SEGMENT='100:' '105:', SELECTION_SEARCH='segment', ; PICK_ATOMS_SET=1, RES_TYPES='all', ATOM_TYPES='all', ; SELECTION_FROM='all', SELECTION_STATUS='initialize' RETURN END_SUBROUTINE
but I have no idea how to extend this to do multiple loop modelling all at the same time... i.e. segment 100-105, 158-164, 200-206, etc... all at once. I've tried lots of things, but I have not been able to figure out the syntax of top too well. I saw an email in the archive by Obdulia Rabal, who used something like
SUBROUTINE ROUTINE = 'select_loop_atoms' READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUENCE, ADD_SEQUENCE = off SET SELECTION_STATUS = 'INITIALIZE' SET SELECTION_MODE = 'ATOM' SET SELECTION_SEARCH = 'SEGMENT' SET SELECTION_FROM = 'ALL' SET GAP_EXTENSION = 2 2 # gaps are extended for two residues in both # directions to get loops (insertions & deletions) PICK_ATOMS SELECTION_SEGMENT = 'LOOPS' RETURN END_SUBROUTINE
but he complained that the program still selected all the atoms for refinement, instead of only the loop portions. I've finally resorted to modelling every single loop separately, but this is no fun at all, and is time consuming. Can someone help please?
Thanks, David
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= David Bostick Office: 262 Venable Hall Dept. of Physics and Astronomy Phone: (919)962-0165 Program in Molecular and Cellular Biophysics UNC-Chapel Hill CB #3255 Phillips Hall dbostick@physics.unc.edu Chapel Hill, NC 27599 http://www.unc.edu/~dbostick =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-