These are both possible. I would write a script that automatically
generates modeller top files. The top file will have a definition to
pick and model loops that are not well refined in the crystallographic
map. You would need a definition how to identify these regions from your
experimental data.->this is a more ab initio approach
Alternatively, you could define a set of "user defined retsraints" from
crystallographic data in general (you will find more about it in the
manual in teh FAQ section). In this second case I would just generate
many models without loop modeling, maybe putting the starting
conformations in a sufficiently "loose" state so you can better explore
and optimize your models ("SET DEVIATION = 6" i.e. in angstroms). ->this
is a more comparative modeling approach
Both approaches assume you have some kind of rough initial model (the
well defined parts of your structure)
However I have not done it, if that is what you are asking for.
best,
Andras
Karsten Suhre wrote:
>
> Right - and what I am seeking is a way of telling Modeller which loops to
> refine on the basis of christallographic data, or maybe another way to
> constrain Modeller with christallographic data. I suppose there are a lot of
> possible ways to do this by hand, depending on the tools you have, but as I
> am still quite new to this domain, I was hoping to find someone who has some
> experience with this in order not to reinvent the wheel.
>
> Kind regards, Karsten.
>
> On Tuesday 27 August 2002 18:04, you wrote:
> > Hello,
> >
> > In case of loop modeling you need to identify the region(s) where you
> > want to apply it, but after that -because it is an ab initio approach-
> > all the generated models are individually optimized samples. Probably
> > that is what you are looking for.
> > It is automatic, beside identifying the segment, you do not need to do
> > anything else.
> >
> >
> >
> > Andras
> >
> > Karsten Suhre wrote:
> > > Hi!
> > >
> > > I am looking for a simple method to score a model from Modeller directly
> > > against raw experimental cristallography data. The idea is to use models
> > > from Modeller for molecular replacement in borderline situations - that
> > > is in situations where the standard cristallographers molecular
> > > replacement tools fail. Thus, the method should be automatic and not
> > > require hand-tuning, so that I can generate lots of different models
> > > (e.g. based on different loop refinement parameters) until I find one
> > > that does the trick. Do you know about someone who already tried this.
> > >
> > > Thank you very much,
> > >
> > > kind regards, Karsten.
> > >
> > > --
> > > Karsten Suhre
> > > Information Genetique & Structurale
> > > UMR CNRS 1889
> > > 31, chemin Joseph Aiguier
> > > F-13402 Marseille Cedex 20
> > > ">mailto:
> > > http://igs-server.cnrs-mrs.fr/~suhre
--
,
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