Dear modellers,
we use Modeller6 and we have some problems restraining beta-sheets in
our model. The student working on this project sent an -email to the
forum a few days ago and since then we have tried many different things
to try to analyze the problem so we send more precise questions.
We tried to restrain beta strands in our model, using the
RESTRAINT_TYPE = 'SHEET' or RESTRAINT_TYPE = 'STRAND' . All our tests
were unsuccessful. Last thing we tried was to force beta strands in the
model to be longer than they are without special restraints. That
means, in the previous model, there are beta strands (they exist in the
template structure) without adding other special restraints in the top
script. I thus think it should be possible to make them slightly longer.
But if I try to apply special restraints to increase their length, the
strands completely disappear in the models.
The .top file is OK, modeller can read it, there are no error messages
in the .log file, the .rsr file contains additionnal restraints
(dihedral pairs) with regards to the same calculation without any
restraint. The .V files are also different with or without the special
restraints. So everything seems to be OK, but the models never contain
these additionnal beta strands. The longer the strands we try to
restrain, the more violations (in the log file) there are but their
magnitude is not significantly higher than when I apply an 'alpha'
restraint (which works perfectly well, i.e. it appears in the model
whatever the region we try to introduce it in). To force strand (or even
beta-sheets) never worked. So it looks like restraining strands and
beta-sheets is much more difficult than alpha-helices, which we can
introduce almost anywhere in the model.
Here are our questions :
Is it normal to be able to force an alpa helix wherever you want and not
a beta, and if yes why ?
Are the violations due to beta strands too penalizing ?
Shall we modify the optimization schedule and if yes, which parameters
should we change ?
Is it possible to exclude block of atoms from the optimization procedure
of the objective function ?
Thanks,
Nathalie Reuter
--
Nathalie REUTER, PhD
U.410 INSERM
Faculte de medecine Xavier Bichat
16, rue Henri Huchard
BP 416
75870 PARIS Cedex 18
tel : (33) 01.44.85.61.32
fax : (33) 01.42.28.87.65
--
Nathalie REUTER, PhD
U.410 INSERM
Faculte de medecine Xavier Bichat
16, rue Henri Huchard
BP 416
75870 PARIS Cedex 18
tel : (33) 01.44.85.61.32
fax : (33) 01.42.28.87.65