The current release of Kojak doesn’t allow for this. However, I just uploaded these changes to the Kojak source tree:
1. Addition of selenocysteine to the amino acid canon (with mass 150.9536303). 2. Ability to add or change the mass of any alphabetical character with the new aa_mass parameter. Usage would be: aa_mass = X 99.545 (to apply a mass of 99.545 to all instances of X in a database). These changes will be rolled out officially in Kojak version 1.6.2. You can take advantage of them now by compiling Kojak from source and replacing the binary in your TPP/bin folder. Comet currently understands selenocysteine. It actually has two unusual amino acids: Selenocysteine: U, mono mass of 150.95363 Ornithine: O, mono mass of 132.08988 It is worth mentioning, though, that O is interpreted to many as Pyrrolysine, which has a much different mass than ornithine. These masses are adjustable in Comet using the add_U_selenocysteine and add_O_ornithine parameters. Cheers, Mike From: spctools-discuss@googlegroups.com [mailto:spctools-discuss@googlegroups.com] On Behalf Of Mariya Indeykina Sent: Wednesday, December 27, 2017 4:56 AM To: spctools-discuss Subject: [spctools-discuss] Selenocysteine in Kojak How can I add an unusual amino acid U for kojak to understand. When I download a human database from swissprot, some proteins carry selenocysteine marked as U. Comet eats these databases with no comments, but kojak says "unexpected amino acid character or errant white space". How can this identifier be added to Kojak and does comet understand this identifier correctly or it just does not show an error? -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
