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Re: strand restraints



If you do not delete the homology derived restraints, they will clash
with the new ones. This might be a problem, but additionally there
always can be some other problems. If you send your example top, and
coordinate file we will take a look.


Andras

Reuter Nathalie wrote:
> 
> 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

-- 
    ,
Andras Fiser, PhD            # phone: (212) 327 7216
The Rockefeller University   # fax:   (212) 327 7540 
Box 270, 1230 York Avenue    # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras