Hi Susy - This issue was raised recently on (I think) the biojava-dev list. The problem is that the MassCalc doesn't deal well (at all) with ambiguity codes.
I think Bruce Waldon suggested a fix. Bruce, do you intend to commit it or should I post a request for enhancement on bugzilla? I think it should be relatively simple to fix. As a work around you could calculate the average values (although this is not terribly practical). - Mark On 4/2/07, Susy Griffiths <[EMAIL PROTECTED]> wrote: > 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.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
