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.
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: owner-modeller_usage@salilab.org > [mailto:owner-modeller_usage@salilab.org] On > Behalf Of Gowthaman R > Sent: Thursday, December 12, 2002 2:50 PM > To: modeller_usage@salilab.org > 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. > >
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: owner-modeller_usage@salilab.org > > [mailto:owner-modeller_usage@salilab.org] On > > Behalf Of Gowthaman R > > Sent: Thursday, December 12, 2002 2:50 PM > > To: modeller_usage@salilab.org > > 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. > > > > > > >
-
Gowthaman R -
Roberto Sanchez