Hi,
This is not a direct answer to your question, yet it may be useful. For loop modeling, either from the scratch or to rebuild, I find RAPPER very useful, either via web interface or stand-alone ( http://mordred.bioc.cam.ac.uk/~rapper/ ). I have scripts for this purpose if anyone is interested in stand-alone version.
The only drawback is that the program requires two "anchor" points that abut the loop, so it won't work for N- or C-terminus modeling.
Take care,
Mensur
At 02:59 PM 8/7/2007, you wrote: >Dear Modeller users, > >I'm refining a conformation of a 6-residue long loop and use the script: > > ># Loop refinement of an existing model > >from modeller.automodel import * > >log.verbose() > >env = environ() > ># directories for input atom files > >env.io.atom_files_directory = './' > ># Create a new class based on 'loopmodel' so that we can redefine > ># select_loop_atoms (necessary) > >class myloop(loopmodel): > ># This routine picks the residues to be refined by loop modeling > >def select_loop_atoms(self): > >self.pick_atoms(selection_segment=('200:A', '205:A'), > >selection_status='INITIALIZE') > >m = myloop(env, > >inimodel='dimer_Cloop_STR_fakeprot_full.pdb', # initial model of the target > >sequence='dimer_Cloop_STR_fakeprot_full') # code of the target > >m.loop.starting_model= 1 # index of the first loop model > >m.loop.ending_model = 500 # index of the last loop model > >m.loop.md_level = refine.slow_large # loop refinement method > >m.make() > > > >Problem 1: > >Is is possible in Modeller to fully optimize the specified loop but also >to allow a little bit of "adjustment freedom" to the loop end residues >(here 199 and 206)? If so, how should I modify the script? > >Problem 2: > >Could anyone advise on the m.loop.md_level? How should I judge what's best >for my loop? > > > >tons of thanks for help and comments > >Agnieszka
========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic@montana.edu | ==========================================================================