hello Dear Roberto Sanchez,
thank you very much for the mail. just few minutes before getting ur mail
i tried the following (which is smillar to what u have suggested) and it
worked. i put '/' chain break instead of '-' in the template. so my
alignment file will look like this....
Template AAAAAAAAAAAA/AAAAAAAAAAAAAAAAAAAAAAAAAAA
Target BBBBBBBBBBBB/----------BBBBBBBBBBBBBBBBB
thanku very much once again sir
with love gowtham
On Thu, 12 Dec 2002, Roberto Sanchez wrote:
> Hi,
>
> It should be enough to replace the region with dashes "-" and have a
> chain break ("/") either right before or after the dashes to make sure
> modeller does not try to pull the flanking residues together. Something
> like this:
>
> Template AAAAAAAAAAAA-AAAAAAAAAAAAAAAAAAAAAAAAAAA
> Target BBBBBBBBBBBB/----------BBBBBBBBBBBBBBBBB
>
> Best,
>
> Roberto
>
> --
> Roberto Sanchez, Assistant Professor
> Structural Biology Program, Department of Physiology & Biophysics and
> Institute for Computational Biomedicine, Mount Sinai School of Medicine
> Box 1677, 1425 Madison Avenue, New York, NY 10029
> phone +1 (212) 659 8648, fax +1 (212) 849 2456
> http://physbio.mssm.edu/~sanchez/
>
>
> > -----Original Message-----
> > From:
> > [">mailto:] On
> > Behalf Of Gowthaman R
> > Sent: Thursday, December 12, 2002 2:50 PM
> > To:
> > Cc: Bozidar Yerkovich
> > Subject: leaving gaps in non aligned regions
> >
> >
> >
> > hello modellers,
> > i am trying to model some proteins. but my protein has some region
> > (internal) (15-20 amino acids) which does not have any
> > corresponding region in the template sequence. i DO NOT
> > want to model that region and in my final (3D) strucuture i
> > want to have a gap in the corresponding internal region.
> > other wise that region forms a loop or extended region (
> > makes the structre ugly ??). i wish to know how my alignement
> > file should look like....
> >
> >
> > i tried following and did not solve the problem
> > 1) putting " X " for the amino acids for which i dont want
> > the 3D structure to be made
> >
> > 2) puting " - " for the same...
> >
> > waiting for ur reply
> >
> > gowthaman
> > Phd Student
> > ICGEB,
> > India.
> >
> >
>
>
>