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
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 | ==========================================================================
Agnieszka Szarecka wrote: > 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?
The residues you select as the loop are optimized, and the remainder of the protein is not moved at all, so there is no real way to "half select" terminal residues in the way you propose. But there are a few things you could try. For example, you could extend the loop selection to include residues 199 and 206, but add additional position restraints on some or all atoms in those two residues to prevent them from moving too much. Alternatively, you could select only some of the atoms (for example, just the sidechain and part of the backbone) from those two residues.
> Problem 2: > > Could anyone advise on the m.loop.md_level? How should I judge what's > best for my loop?
Generally speaking, the longer the refinement you can afford, the better. But for longer loops the limiting factor is almost certainly the conformational sampling, which is probably easier to control by building more models rather than longer refinement.
Ben Webb, Modeller Caretaker
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Agnieszka Szarecka -
Mensur Dlakic -
Modeller Caretaker