Hi All,
I want to model a complex A1+B1 on a template complex A+B where A and B
are proteins. I have only one template available.
Does somebody as a warking script to do this?
Many thanks
Edo
--
Dr Edoardo Saccenti
CERM Magnetic Resonance Center
University of Florence
Fiorgen Foundation
Via Luigi Sacconi n° 6
50019 Sesto Fiorentino
(FI) Italy
Tel: +39 055 4574281
I am trying to incorporate some experimentally-derived distance
restraints into a homopentamer model, and had a few questions:
1.) the manual says that restraints.make_distance() should be used for
setting physical distance restraints. However,in the section on
restraints.add() http://salilab.org/modeller/manual/node209.html, an
example is given on setting distance restraints with this instead of
restraints.make_distance(). Is there any benefit to using one versus the
other? Do you use the rsr.add() if you have a lot of restraints to add
(as I do- 15 in all)?
2.) restraints.make_distance() uses an analytic model to calculate
standard deviations, and the manual says to use model 5 for
Calpha-Calpha distances and model 6 for N-O distances. I have not been
able to find a description of these models, or which one to use for
other atom-pair distances. Does it really make much difference?
I did try a quick modeling using restraints.add with the following line
in the script:
rsr.add(forms.gaussian(group=physical.xy_distance,feature=features.distance(at['ND2:93'],at['NH1:905']),mean=19.3,stdev=0.2))
and got the following error message:
**************************************************************************
File "EnforceSymmetryTrim_distance_restraints.py", line 96, in ?
a.make()
File "/usr/lib/modeller9v2/modlib/modeller/automodel/automodel.py", line
99, in make
self.homcsr(exit_stage)
File "/usr/lib/modeller9v2/modlib/modeller/automodel/automodel.py",
line 423, in homcsr
self.mkhomcsr(selection(self), aln)
File "/usr/lib/modeller9v2/modlib/modeller/automodel/automodel.py",
line 506, in mkhomcsr
self.special_restraints(aln)
File "EnforceSymmetryTrim_distance_restraints.py", line 37, in
special_restraints
feature=features.distance(at['ND2:93'], at['NH1:905']),
File "/usr/lib/modeller9v2/modlib/modeller/coordinates.py", line 137,
in __getitem__
(self.offset, self.length, self.suffix))
File "/usr/lib/modeller9v2/modlib/modeller/util/modutil.py", line 19,
in handle_seq_indx
int_indx = lookup_func(*args)
File "/usr/lib/modeller9v2/modlib/modeller/coordinates.py", line 47,
in _indxatm
raise KeyError, ("No such atom: %s" % indx)
KeyError: 'No such atom: ND2:93'
*************************************************************************
which suggests that it can't find the ND2 atom in residue 93 . However,
the atom does exist in the *.ini file (as does atom NH1 in residue 905):
ATOM 783 ND2 ASN A 93 30.499 39.522 -12.905
ATOM 7622 NH1 ARG E 905 45.372 32.420 -16.993
any ideas as to what is going on here?
Thanks
Mike White
Hi
I was wondering if it was possible, given two protein sequences or
structures, to show possible docking interactions between the two
proteins? And if so, how this is done??
Thanks for your time, Ryan
