Loop modelling in a large system

[Graham tyrrell <tyrrell AT yorvic.york.ac.uk>]

Dear Modellers,

I am attempting to use Modeller to model a number of loops into a very
large protein system, and am having a few problems. (I am relatively new

to Modeller so please excuse any dumb questions)

I have 4 suitable structures which I wish to use as templates for the
missing loop regions in my main structure. The problem I have is that I
want to constrain the coordinates of my model to a greater extent
towards
that of the template which has the loops missing, I then want to use the

remaining templates to build in the loops.

This seems a similar problem to one described in the FAQ:
('5. I don't want to use one region of a template for construction of my
model')
however, due to the large number of loops missing,
and the length of my sequence (~1000 residues) this would be extremely
laborious, with plenty of room for error.

I was wondering if anyone had any similar experience, and could advise
me
as to an appropriate strategy.

Regards,

Graham Tyrrell


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Graham Tyrrell          Email   (Work)     : tyrrell AT yorvic.york.ac.uk
                                (Personal) : gpt103 AT york.ac.uk

                        Telephone          : (01904) 432550
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