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RE: leaving gaps in non aligned regions



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.
> 
>