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RE: leaving gaps in non aligned regions



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.
> > 
> > 
> 
> 
>