Actually..... im now getting this error
------------------------------
*0 total peptides, 0 unique stripped peptides*
Legacy Viewer worked on one sample. If I look at ProtXML I have lots of
peptides so im not sure why im getting this error.
On Friday, December 2, 2016 at 9:04:33 AM UTC-5, Kevin Hart wrote:
>
> I reinstalled TPP 5.0 in the correct directory and legacy viewer is now
> working. Thank you for working through all of this with me
>
> On Wednesday, November 30, 2016 at 5:07:41 PM UTC-5, Luis wrote:
>>
>> Hi Kevin,
>> Do you have 2 versions of TPP installed concurrently on the same
>> machine? It looks like the installation of 5.0 was done with "C:\TPP\"
>> specified as the data directory; but you are using data in the previous TPP
>> data directory "C:\Inetpub\wwwroot\ISB\" .
>>
>>
>> One quick way to get this fixed and allow you to use the legacy viewer is
>> the following:
>>
>> 1. Open the file C:\TPP\cgi-bin\protxml2html.pl -- in Notepad or your
>> favorite text editor.
>>
>> 2. Scroll down to around line 44, just *after *the line that says use
>> tpplib_perl; # exported TPP lib function points
>>
>> 3. Add the following *new *line:
>> *$ENV{'WEBSERVER_ROOT'} = 'C:/Inetpub/wwwroot/ISB/';*
>>
>> 4. Save this file.
>>
>> 5. Finally, if the following file exists, delete it* (please match the
>> file ending carefully!!)
>> C:/Inetpub/wwwroot/ISB/data5.0/SEL55/SEL55.Comet.Tandem.interact.prot.
>> *xsl*
>>
>> * You should likewise delete any other existing .xsl files if you find any
>> trouble opening its corresponding prot.xml file
>>
>>
>> You should now be able to use the legacy viewer with any file that is
>> located in this data area. Do note that this is a bit of a temporary fix,
>> and I recommend that you reinstall TPP 5.0 with the correct settings at a
>> future date, or when/if you update to the next version, once we release it.
>>
>> Hope this helps!
>>
>> --Luis
>>
>>
>> On Wed, Nov 30, 2016 at 10:55 AM, Kevin Hart <[email protected]>
>> wrote:
>>
>>> Gladly. On our machines were not getting an error it just simply will
>>> not generate a page. The page is completely blank. Attached are both files
>>> so you can take a look.
>>>
>>> On Tuesday, November 29, 2016 at 4:34:50 PM UTC-5, Luis wrote:
>>>>
>>>> The new viewer has been updated to display and export protein length.
>>>> It will be included in the next release of TPP, but I'd be glad to forward
>>>> you an advance copy so that you can get to your data.
>>>>
>>>> And I have not been able to see what's wrong with the legacy viewer; I
>>>> just tested it in 3 different machines and seems to be working. Can you
>>>> share your protXML file so I can try to debug? Furthermore, if there is a
>>>> problem with the code, an error might have been logged to the web server
>>>> error log; you can explore this by opening the file httpd-error.log,
>>>> typically found under C:\TPP\log\ . Or if you don't mind sharing this
>>>> file, I can have a look.
>>>>
>>>> Cheers,
>>>> --Luis
>>>>
>>>>
>>>> On Tue, Nov 29, 2016 at 5:20 AM, Kevin Hart <[email protected]>
>>>> wrote:
>>>>
>>>>> Do you know how to get it to export protein length with the .tsv file
>>>>> from ProtXML?
>>>>>
>>>>>
>>>>> On Wednesday, November 23, 2016 at 3:52:08 PM UTC-5, Kevin Hart wrote:
>>>>>>
>>>>>> I can see both tables and graphical models. My files were not where
>>>>>> TPP thought they were and thus confusion arose when I clicked on models
>>>>>> in
>>>>>> ProtXML. ProtXML just didnt know where to look.
>>>>>>
>>>>>> Legacy Viewer was nice because I was able to select different things
>>>>>> to be displayed like protein length and all of those other toggles. I
>>>>>> cant
>>>>>> find a way in ProtXML to have it export those other things for me so I
>>>>>> can
>>>>>> generate SAF and NSAF values.
>>>>>>
>>>>>> On Wednesday, November 23, 2016 at 1:26:24 PM UTC-5, Luis wrote:
>>>>>>>
>>>>>>> That's great. Can you only see the tables? Or also the graphical
>>>>>>> models?
>>>>>>>
>>>>>>> The legacy viewer is being phased out in favor of the new one, and
>>>>>>> is slated for removal from distribution. Is there a specific function
>>>>>>> that
>>>>>>> you need from it that the new one does not have?
>>>>>>> If you really need it soon, you could install a previous version of
>>>>>>> TPP on a different computer and open your file there.
>>>>>>>
>>>>>>> --Luis
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Nov 23, 2016 at 9:10 AM, Kevin Hart <[email protected]>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> I am able to gain access now to the error sensitivity tables but
>>>>>>>> still need access to legacy viewer.
>>>>>>>>
>>>>>>>>
>>>>>>>> On Monday, November 21, 2016 at 11:42:45 AM UTC-5, Kevin Hart wrote:
>>>>>>>>>
>>>>>>>>> I downloaded and am using the new version of TPP(5.0) on Windows 7
>>>>>>>>> however im running into a small issue. I can not access the
>>>>>>>>> error/sensitivity tables through both ProtXML Viewer (Forbidden You
>>>>>>>>> don't
>>>>>>>>> have permission to access
>>>>>>>>> /tpp/data/SEL42/SEL42.Tandem.Comet.interact.prot-MODELS.html on this
>>>>>>>>> server.) and legacy viewer is not loading at all. Unfortunately I
>>>>>>>>> need
>>>>>>>>> these things to run all of my analysis. If anyone would have a work
>>>>>>>>> around
>>>>>>>>> or fix for this I would appreciate it.
>>>>>>>>>
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>>>>>>>>
>>>>>>>
>>>>>>> --
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>>>>>
>>>>
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>>
>>
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