Dear Marc, The difference is Havg = 1.00794 (see cvs). You calculated the mass MH+ (M plus one ionization H+), which - I guess - is used for mass spectrometry analysis.
Regards, George -----Original Message----- From: Marc Savitsky [mailto:[EMAIL PROTECTED] Sent: Wednesday, April 18, 2007 5:41 AM To: george waldon Subject: Re: Biojava MassCalc Hi George, I had some time to look at the MassCalc.getMolecularWeight(protein) method, and it does to job with regard to ambiguous symbols. Are you aware that it doesn't return the same value as getMass() for sequences without ambiguous codes? My test case examines the sequence AASLIKPCAYEKQGLIDHAIGSYKVLHDKISESYYKVISRRLERYGIVLDLNGVKEIVKDVVVLHDMGKAGEYYQNQFDDNC NPLKSNPLKSRFSFIYHELGSALFFYNDYEPINVEKAEEVRSLLTLAVINHLNAIRGISDYLLNRFPDNFDEEMIKLSKYGSILLE NLRGIISKSLKVRDYSFTDYHDMLYAFSKKSDKYLKLYNLFLAPIMLGDNLDSSLVRNNGSKTRFVGILEGELNGGSTLCCCC but getMass returns a value of 28633.94392000000152620486915111541748046875 whereas getMolecularWeight returns 28632.9359800000020186416804790496826171875. regards Marc Savitsky _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
