If you mean how to compile Kojak, this perhaps isn’t the easiest thing to do, and it cannot be done from the TPP GUI. It requires downloading the source tree, and the supporting library source trees, then building the libraries and application with a compiler. Your choice of compiler will dictate what instructions to follow and might be beyond the scope of this forum. The code is all available from http://kojak-ms.org
However, as an alternative, you can wait for Kojak 1.6.2 to be officially released. You can then download the latest official Kojak and overwrite your TPP Kojak. In Windows, replace C:\TPP\bin\Kojak.exe with the newer Kojak.exe. The process is the same in Linux, but with the Linux binary. Once updated, you can easily add the parameters inside the GUI by navigating to the Kojak configuration file in the TPP File Browser. Select “Edit” from the link next to the configuration file, then add the new parameters to your configuration file. Save the changes and proceed with your Kojak analysis. From: [email protected] [mailto:[email protected]] On Behalf Of Maria Indeykina Sent: Thursday, December 28, 2017 1:11 PM To: [email protected] Subject: RE: [spctools-discuss] Selenocysteine in Kojak Thanks, Mike. For a stupid GUI user, how can this be done? _____ From: Michael Hoopmann <mailto:[email protected]> Sent: 28.12.2017 23:29 To: [email protected] Subject: RE: [spctools-discuss] Selenocysteine in Kojak 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: [email protected] [mailto:[email protected]] 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 [email protected]. To post to this group, send email to [email protected]. 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 [email protected]. To post to this group, send email to [email protected]. 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 [email protected]. To post to this group, send email to [email protected]. 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
