Hi Susy, As I am reading your mail, a fix is already implemented in the cvs for molecular weight calculation of polypeptides containing ambiguity symbols. I haven't done anything for pKs but I can get a look at this. Give me a few days.
George (not Bruce!) -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Susy Griffiths Sent: Monday, April 02, 2007 6:04 AM To: [email protected] Subject: [Biojava-l] Calculate mass and pI for a protein containingambiguity symbols Hi, how can I avoid the IllegalSymbolException to calculate the mass and pI of a protein using BioJava, when the sequence contains 'X' or 'B' or 'Z'? The Expasy comput pI /Mw tool does this, see http://us.expasy.org/tools/pi_tool-doc.html "In addition to the standard one-letter-codes for the 20 amino acids, the characters B, Z and X are accepted: B Asx Aspartic acid or Asparagine Z Glx Glutamine or Glutamic acid X Xaa Any amino acid The mass values used for these residues are mean values of the corresponding masses, and B, Z and X are presumed to have pK values of 0, i.e. a pI of 5.52." Would I need to edit the ResidueProperties.xml file to provide average mass entries for X, B & Z ? thanks, Susy -- ********************************************************* Dr S.L. Griffiths YSBL Department of Chemistry University of York Heslington York YO10 5YW UK http://www.pims-lims.org/ email: [EMAIL PROTECTED] Tel. +44 (0)1904 328270 Fax +44 (0)1904 328266 ********************************************************* _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio. _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
