[Biojava-l] error using the proteomic package

[Keith James]

>>>>> "Robert" == Robert Stones <r.stones at csl.gov.uk> writes:

    Robert> I keep getting this error using the proteomic package when
    Robert> performing simulated digests on proteins and some peptides
    Robert> with masses are not being generated:

    Robert> Has anybody got an example code for setting proteases and
    Robert> working out masses?

    Robert> org.biojava.bio.symbol.IllegalSymbolException: No mass Set
    Robert> for Symbol [GLU SER GLY PHE LEU PRO ALA VAL ASN SEC HIS
    Robert> MET THR TYR ARG ILE LYS GLN TRP CYS ASP] at
    Robert> org.biojava.bio.proteomics.MassCalc.getVMasses(MassCalc.java:365)

That stringified Symbol looks like an ambiguity symbol for all amino
acids. Do your proteins have X's in them?

Looking at the code is seems that masses are set for unambiguous
residues, but there is no fancy estimation of mass ranges based on
ambiguities.

Keith

-- 

- Keith James <kdj at sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -