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
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| Mensur Dlakic, PhD | Tel: (406) 994-6576 |
| Department of Microbiology | Fax: (406) 994-4926 |
| Montana State University | |
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