Get MolecularFormula from Selenocysteine containing peptide

[cctsou]

Hi,

I am trying to generate MolecularFormula from a rare Selenocysteine containing peptide using the following codes.

String pepseq="AASUBR";
AASequenceImpl aaseq=new AASequenceImpl(pepseq);
MolecularFormula formula = new MolecularFormula(aaseq);

It threw null exception at MolecularFormula() where it seems like elements.txt does not have definition for amino acid U (Selenocysteine). Since selenocysteine has Se element which is not listed in the top of elements.txt so I figured it may take more efforts to add this amino acid. Could you help me or guide me where should I modify the codes make it worked?

Thanks a lot,

[mvaudel]

Hi,

Sorry this is some rather old code, may we get some more input on what you want to do?

Would AminoAcidSequence do what you need?

Best regards,

Marc

[cctsou]

Hi Marc,

Thank you for the response, I am using it for for calculating isotope pattern.

AASequenceImpl AAimple=new AASequenceImpl(Sequence);
formula=new MolecularFormula(AAimple);
IsotopicDistribution calc = new IsotopicDistribution(formula);   

Is it possible to generate MolecularFormula from AminoAcidSequence?

Thanks, Chih-Chiang

[mvaudel]

Hi Chih-Chiang,

No sorry, I will need to check with the developers of this part of the code. We will keep you posted.

Apologies for the inconvenience,

Marc

[hbarsnes]

Hi Chih-Chiang,

We've just deployed utilities version 4.11.6 which adds the required support for Selenocysteine (thanks to @nielshulstaert). Please give the new version a go and let us know if you come across any new issues.

Best regards, Harald

[cctsou]

Hi Harald,

It's awesome, thanks a lot.

Best, Chih-Chiang