Hi Joe, The Pep3D URL for the mzXML file in petunia is: http://cvid.som.umaryland.edu:8080/tpp/cgi-bin/Pep3D_xml.cgi?htmFile=/usr/local/tpp/data/projects/s-aorta-1/121205_Saorta1_Guan-8.mzXML
Clicking on this presents the PeP3D parameters page with the following in the file path box: /usr/local/tpp/data/projects/s-aorta-1/121205_Saorta1_Guan-8.mzXML after clicking "generate Pep3D image" the contents of the file path box change to: /usr/local/tpp/data/projects/s-aorta-1/121205_Sarta1_Guan-8.mzXML (note the missing o in Saorta) In the messages box I get the following: Generating images... Error: Only pepxml, .mzData or .mzXML file is accepted! Second method: If I click on the pep.xml link which has this URL: http://cvid.som.umaryland.edu:8080/tpp/cgi-bin/PepXMLViewer.cgi?xmlFileName=/usr/local/tpp/data/projects/s-aorta-1/121205_Saorta1_Guan-8.tandem.pep.xml On the PepXML viewer page, the file path box contains: /usr/local/tpp/data/projects/s-aorta-1/121205_Saorta1_Guan-8.tandem.pep.xml I then click "other actions" and "generate Pep3D" I get the Pep3D parameters page with the following in the file path box: /usr/local/tpp/data/projects/s-aorta-1/121205_Saorta1_Guan-8.tandem.epp.xml (note the inversion of .pep to .epp) Whether I correct the epp back to pep before hitting "generate Pep3D image" or not, it will also remove the "o" as above, revert back to .epp as well and fail. Let me know if you need further information. Thanks, Brian On Mon, Dec 17, 2012 at 2:28 PM, Joseph Slagel < [email protected]> wrote: > Brian, > > How are you getting to the Pep3D viewer. Are you clicking on the Pep3D > link in the petunia browser or are you clicking on the "Generate Pep3D" > button in the pep.xml viewer. > > -Joe > > > On Fri, Dec 7, 2012 at 6:44 AM, Brian Hampton <[email protected]>wrote: > >> I am seeing a strange behavior in TPP 4.6.1 (also saw same in 4.5.2) >> Linux install. When I click on the link to generate a Ped3D image of >> either an .mzXML file or a pep.xml file it will re-write the file name and >> then not be able to generate the Pep3D image cause a file with that name >> doesn't exist. For example: >> >> /usr/local/tpp/data/projects/s-aorta-1/121205_Saorta1_Guan-6.mzXML is the >> input file to Pep3D and it will re-write the file name to: >> >> /usr/local/tpp/data/projects/s-aorta-1/121205_Sarta1_Guan-6.mzXML and >> then fail cause that file doesn't exist. Note the missing "o". >> >> If I keep clicking the button to generate the Pep3D image it will >> continue to delete certain letters and then I got this: >> >> >> /usr/local/tpp/data/projects/s-aorta-1/121205_Saa1_Guan-6.mzXMLmzRange=Full >> >> The mzXML files are generated by MSConvert on a PC from a thermo .raw >> file no options other than 32 bit. >> >> Any clues? >> >> Thanks in advance, >> >> Brian >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
