Hi, David: renaming the .new.mzXML files gives me the same error message as my screenshot (http://flic.kr/p/av3Rjm) when I try to convert it to a Pep3D image. I am not sure how I got my first Pep3D image above.
>From my understanding, I am suppose to access the pepXML viewer from .pep.xml files correct? I am stuck trying to load the link localhost/tpp-bin/PepXMLViewer.cgi?xmlFileName=c:/Inetpub/wwwroot/ISB/ data/tutorial/raft4041.pep.xml (I have all of the .pep.xml files in my Tutorial folder) because it it shows me a blank screen as though it is trying to load the page but the page remains blank for over 15 minutes. Meanwhile, I will experiment with the TPP Demo 2009 (http:// tools.proteomecenter.org/wiki/index.php?title=TPP_Demo2009) and keep you updated. Thanks for all of your help. Regards, Chris On Oct 11, 3:52 pm, Chris L <li...@uci.edu> wrote: > Update: the image file showed up after a couple minuteshttp://flic.kr/p/av4925 > > Chris > > On Oct 11, 3:42 pm, Chris L <li...@uci.edu> wrote: > > > > > > > > > Thank you for your help Luis, > > > TPP does not look for .mzXML files after I did the re-index operation > > and instead looks for .new.mzXML files so I ended up not renaming the > > files. > > Now the problem is that the [View] option from the log disappeared and > > is replaced with a [Pep3D] option (screenshot herehttp://flic.kr/p/av1izP) > > I have trouble converting the new files to Pep3D > > image:http://flic.kr/p/av3Rjm > > Also, when I tried to manually access the PepXML viewer page manually > > as shown in tutorial, I get the following screen:http://flic.kr/p/av3RjW > > Is the new TPP still compatible with PepXML viewer or are we limited > > to Pep3D for now? > > Sorry for all the problems I am asking and thanks again. > > > Regards, > > Chris > > > On Oct 7, 1:52 pm, Luis Mendoza <luis.mend...@systemsbiology.org> > > wrote: > > > > Hi Chris, > > > It turns out that the mzXML files included for this tutorial have a > > > corrupt > > > index, which makes the new versions of our tools throw an error. Since > > > this > > > tutorial was provided and the data is hosted by external collaborators, I > > > will contact them to ask them to update the data files. > > > > In the meantime, you can fix the mzXML files in the following way: > > > > - In Petunia (the GUI), go to the "Index mxXML Files" page, found under > > > the > > > "mzXML Utils" tab. > > > - Select all 6 mzXML files in the Tutorial folder, then hit the > > > "Re-Index..." button. > > > - This will create files named "raft4041.new.mzXML" etc. You will need to > > > RENAME these .new files to the original file names (i.e. get rid of the > > > ".new" part) -- do this under Windows Explorer (you may need to either > > > delete or move the original files, as the names will collide). > > > > You should at this point be able to continue working on the conversion > > > step > > > of the tutorial; please let us know if this does not work. > > > > I would also recommend following the Tandem tutorial that we have linked > > > from the top of that page. > > > > Cheers, > > > --Luis > > > > On Fri, Oct 7, 2011 at 8:36 AM, Chris L <li...@uci.edu> wrote: > > > > Hi again, > > > > I am trying to follow the SEQUEST data analysis tutorial in the > > > > following link > > > >http://tools.proteomecenter.org/wiki/index.php?title=TPP_Tutorial > > > > I am having problem with opening my converted pepXML files in pepXML > > > > viewer. > > > > Below are the screenshots of what is happening (click on the picture > > > > to zoom in): > > > > This screenshot shows my conversion settings > > > >http://flic.kr/p/atDywi > > > > This is the log file I got after the commands are completed (same with > > > > all six output files) > > > >http://flic.kr/p/atGeEs > > > > Here's what happens when I tried to opening one of them via the "View" > > > > option in the output files pane > > > >http://flic.kr/p/atDyh8 > > > > Any suggestion is appreciated. Thanks! > > > > > Regards, > > > > Chris > > > > > On Oct 7, 8:13 am, Chris L <li...@uci.edu> wrote: > > > > > Hi Luis, > > > > > > Yes, I overlooked it. Setting it to SEQUEST solved the problem. Thanks > > > > > a lot! > > > > > ps. It is my first time using TPP, so I get to have some leeway > > > > > right? :) > > > > > > Regards, > > > > > Chris > > > > > > On Oct 6, 5:52 pm, Luis Mendoza <luis.mend...@systemsbiology.org> > > > > > wrote: > > > > > > > Hi Chris, > > > > > > Which tutorial are you referring to? Please also note that you must > > > > set the > > > > > > "pipeline type" to "Sequest" on the home page if you wish to convert > > > > .out > > > > > > files to pepXML; leaving it set to "Tandem" will tell the software > > > > > > to > > > > only > > > > > > look for files of that type. > > > > > > Cheers, > > > > > > --Luis > > > > > > > On Thu, Oct 6, 2011 at 5:48 PM, Chris L <li...@uci.edu> wrote: > > > > > > > Dear all, > > > > > > > > I am attempting the tutorial steps for TPP. The tutorial > > > > > > > instructed > > > > me > > > > > > > to choose .out files to convert to pepXML; however, the TPP shows > > > > > > > it > > > > > > > cannot detect compatible file (.tandem) I am wondering whether I > > > > > > > am > > > > > > > suppose to convert .out files into .tandem files, or should I try > > > > > > > downloading .tandem files somewhere? Any input is appreciated. > > > > > > > Thank > > > > > > > you. > > > > > > > > Sincerely, > > > > > > > Chris L > > > > > > > > -- > > > > > > > You received this message because you are subscribed to the Google > > > > Groups > > > > > > > "spctools-discuss" group. > > > > > > > To post to this group, send email to > > > > spctools-discuss@googlegroups.com. > > > > > > > To unsubscribe from this group, send email to > > > > > > > spctools-discuss+unsubscr...@googlegroups.com. > > > > > > > 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 spctools-discuss@googlegroups.com. > > > > To unsubscribe from this group, send email to > > > > spctools-discuss+unsubscr...@googlegroups.com. > > > > 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. 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