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.
>
>