Dear Graham,
If you wish to use only a certain segment (loop) from a given template
sequence/structure and the rest should be built rather on another template(s)
than you should look at FAQ 4 and 5 as you already guessed it. You are right,
that in case of several loops this requires a lot of attention when creating
the "misalignments". This approach is neccesary beause the program needs to
know a continuous stretch of residues otherwise, if you only "patching" small
loop segments in the alignment, the program doesn't know which coordinates
belong to which residue. Hopefully in the future we will find a more suitable
solution.
When creating the alignment use the PAP format. That helps.
best wishes,
Andras
Graham tyrrell wrote:
>
> 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
>
> --
> ----------------------------------------------------------------------
> Graham Tyrrell Email (Work) :
> (Personal) :
>
> Telephone : (01904) 432550
> -----------------------------------------------------------------------
--
,
Andras Fiser, PhD # phone: (212) 327 7206
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras