Hi Graham,
It is not clear to me what exactly your situation is. Do you want to use
the "loop templates" only for the loops and discard the rest of the
structure? Or do you want to use those template also for the rest of the
structure but you would like to give a higher weight to the template
without the loops?
In the first case you could do what is suggested in FAQ #5 as you
mentioned. You are right that this might be cumbersome in your case. An
alternative is to treat each loop as a separate template. Let's say
template X has two loops that will be used; residues 10-15 and 25-30. If
Y is the "loop-less" template the alignment (PIR format) would look
something like this:
P1;X1
structure:X:10::15:::::
---------XXXXX------------------------------------------------------*
P1;X2
structure:X:25::30:::::
------------------------XXXXX---------------------------------------*
P1;Y
structure:Y:1::50:::::
YYYYYYYYY-----YYYYYYYYYY-----YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY*
P1;target
sequence:target::::::::
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT*
In this case it is important that there is some overlap between the loop
region of X (X1 and X2) and the template Y in the alignment. The anchor
residues of the loops should be aligned with the corresponding residues
in Y to make sure MODELLER gets the relative orientation of the loops
correctly.
The second case is simpler. If you can use the full structure of the
loop templates (i.e. the loop templates are homologues of the target
sequence) but you want the "loop-less" template to have a bigger weight
you can simply add more copies of this template to the alignment. It
would be like this:
P1;X
structure:X:1::60:::::
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX*
P1;Y1
structure:Y:1::50:::::
YYYYYYYYY-----YYYYYYYYYY-----YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY*
P1;Y2
structure:Y:1::50:::::
YYYYYYYYY-----YYYYYYYYYY-----YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY*
P1;Y3
structure:Y:1::50:::::
YYYYYYYYY-----YYYYYYYYYY-----YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY*
P1;target
sequence:target::::::::
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT*
In this case Y would have three times the weight of X in the non-loop
regions.
I hope this helps.
Best Wishes,
Roberto
--
Roberto Sanchez | phone : (212) 327 7206
The Rockefeller University | fax : (212) 327 7540
1230 York Avenue, Box 38 | e-mail:
New York, NY 10021-6399 | http://salilab.org
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
>
> --
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> Graham Tyrrell Email (Work) :
> (Personal) :
>
> Telephone : (01904) 432550
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