[Biojava-l] Calculate mass and pI for a protein containing ambiguity symbols

Mark Schreiber markjschreiber at gmail.com
Mon Apr 2 14:38:48 UTC 2007

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

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 <susy at ysbl.york.ac.uk> 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
> Department of Chemistry
> University of York
> Heslington
> York
> YO10 5YW
> UK
> http://www.pims-lims.org/
> email: susy at ysbl.york.ac.uk
> Tel. +44 (0)1904 328270
> Fax +44 (0)1904 328266
> *********************************************************
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