In general it's not possible to accurately reconstruct a protein's backbone strictly from phi/psi angles--you'd need the bond lengths and bond angles (especially important) to have an accurate reconstruction. It is however possible to get an approximate reconstruction, particularly for short protein fragments, if you use "standard" values for bond lengths and angles, such as the ones here:
http://scripts.iucr.org/cgi-bin/paper?li0061 I don't know if biojava has any methods specific for this purpose, but the link below contains a description of how to reconstruct the coordinates if you have the dihedral angles (and bond lengths and angles) that doesn't require more functionality than simple 3D transforms: https://lists.sdsc.edu/pipermail/pdb-l/2002-December/000326.html Hope this helps, Mohammed --- Mohammed AlQuraishi McAdams and Shapiro Labs Stanford University -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Andreas Prlic Sent: Friday, July 18, 2008 7:05 AM To: Richard Holland Cc: biojava-1 mailing list Subject: Re: [Biojava-l] Constructing Backbone of Protein Hi Richard, This email actually managed to find its way through to the list back in May... http://www.biojava.org/pipermail/biojava-l/2008-May/006211.html Andreas On 17 Jul 2008, at 20:15, Richard Holland wrote: > Not sure. Andreas Prlic should know. Andreas....? > > 2008/5/13 Armita Sheari <[EMAIL PROTECTED]>: >> Hi everyone, >> >> I need to write a program that can construct the backbone of the >> protein >> from its sequence and the relevant phi and psi angles. I want to >> know if >> there is a class or method that can help me to calculate the >> coordinates >> form phi and psi angles! >> >> thanks, >> ArmitaSh >> >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> >> ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
