Hi, I have a problem with the model building. Specifically, I have the coordinates of the backbone and I want to add its sidechains but I can't find the appropriate script. If someone knows the name of the script, tell me. Thank you in advance, Maria.
Modeller should be able to do this, but if your intent is to just add sidechains and not change backbone at all, I would suggest SCWRL:
http://dunbrack.fccc.edu/SCWRL3.php
Other useful servers:
http://bioserv.rpbs.jussieu.fr/cgi-bin/SCit http://eudoxus.scs.uiuc.edu/r3.html http://irecs.bioinf.mpi-inf.mpg.de/
At 03:45 AM 5/28/2008, matziast@med.uth.gr wrote: >Hi, >I have a problem with the model building. Specifically, I have the coordinates >of the backbone and I want to add its sidechains but I can't find the >appropriate script. If someone knows the name of the script, tell me. >Thank you in advance, >Maria. >_______________________________________________ >modeller_usage mailing list >modeller_usage@salilab.org >https://salilab.org/mailman/listinfo/modeller_usage
========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | Lab: (406) 994-6237 | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic@montana.edu | ==========================================================================
matziast@med.uth.gr wrote: > I have a problem with the model building. Specifically, I have the coordinates > of the backbone and I want to add its sidechains but I can't find the > appropriate script.
The complete_pdb() script will automatically add in sidechains from internal coordinates. You'll probably then want to optimize the sidechain positions and allow the backbone to relax, with some optimization. One such script to do that is at http://salilab.org/modeller/9v4/manual/node246.html
As Mensur points out, if you don't need the backbone to relax, it could well be more efficient to use SCWRL.
Ben Webb, Modeller Caretaker
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matziast＠med.uth.gr -
Mensur Dlakic -
Modeller Caretaker