[spctools-discuss] Re: upcoming Windows TPP dependency: ActivePerl 5.8.8

2008-10-17 Thread Chee-Hong Wong
Just a thought: it will be most convenient for user If the installer can pop up a dialog where its text has hyperlink to the ActiveState download site. *Chee-Hong. On Fri, Oct 17, 2008 at 1:34 PM, Natalie Tasman <[EMAIL PROTECTED]>wrote: > Hello all, > > With the native Windows installer in the T

[spctools-discuss] Re: ReAdW-4.0.2 execution problem

2008-10-17 Thread Natalie Tasman
Also, you can run the program from the TPP web interface (Petunia), if you like. Natalie On Fri, Oct 17, 2008 at 1:02 PM, Jimmy Eng <[EMAIL PROTECTED]> wrote: > > Carsten, > > That binary is a command line app so you just can't double click on it > to run. On the command line, execute the binar

[spctools-discuss] upcoming Windows TPP dependency: ActivePerl 5.8.8

2008-10-17 Thread Natalie Tasman
Hello all, With the native Windows installer in the TPP 4.0.x series, a version of the Perl language was installed automatically if an apropriate one was not found. We've found that there is a much better solution than for us than to try to maintain our own custom Windows Perl installation, which

[spctools-discuss] Re: ReAdW-4.0.2 execution problem

2008-10-17 Thread Jimmy Eng
Carsten, That binary is a command line app so you just can't double click on it to run. On the command line, execute the binary to see a usage statement with all options. Minimally, you would do something like the following to convert your file: readw.exe somefile.RAW Carsten wrote: > H

[spctools-discuss] Re: trouble exporting PIPE to file

2008-10-17 Thread Natalie Tasman
Hi Kristian, I'm sure that Hector will reply with more information, but please do try with firefox. Most of our applications are primarily tested with this browser, and any gaggle/firegoose functionality for PIPE or the TPP tools requires firefox (firegoose is a firefox extension.) (You'll want

[spctools-discuss] Re: mzWiff conversion for mascot searches

2008-10-17 Thread Matthew Chambers
First, let me inform the list that ABI has their own mzML exporter (aptly named mzML_Exporter) that is currently in private beta testing. It provides free access (but not open source) to WIFF data. It doesn't depend on Analyst or on Protein Pilot. It can provide raw profile data, or it can do

[spctools-discuss] Re: ProteinProphet

2008-10-17 Thread Brian Pratt
Thanks for the report - that was fixed yesterday in SVN 3714 (trunk is a moving target!). Brian _ From: spctools-discuss@googlegroups.com [mailto:[EMAIL PROTECTED] On Behalf Of Abhishek Pratap Sent: Thursday, October 16, 2008 2:42 PM To: spctools-discuss@googlegroups.com Subject: [

[spctools-discuss] Re: no output when running ProteinProphet

2008-10-17 Thread David Shteynberg
It might also be the case that there are just very few positive ids in your search results either due to data quality or search parameters that either include or exclude some important static modification. To check the data quality you can look at your mzXML files in Pep3D. Please double check th

[spctools-discuss] Re: no output when running ProteinProphet

2008-10-17 Thread David Shteynberg
It looks like PeptideProphet's quality check fail and throw out some potentially good models. Try rerunning the tool with the option to force the output of the models. On Fri, Oct 17, 2008 at 5:06 AM, John Lee <[EMAIL PROTECTED]> wrote: > > Anyone else met this problem? > > > > > --~--~

[spctools-discuss] trouble exporting PIPE to file

2008-10-17 Thread Kristian
Hi Hector- I've been using PIPE and finding it very useful, but I've had some trouble exporting my data. I am running Internet Explorer 7 with Google toolbar. If I attempt to export my PIPE data set when I have pop-ups disabled, I am then given the option to view the blocked pop-up, which is my

[spctools-discuss] Re: ProteinProphet

2008-10-17 Thread Abhishek Pratap
using the latest SVN, rev 3711 After TPP I dont see an interact.prob.pep.shtml there. Also opening the file interact.prob.shtml hangs my browser but the file it not large. Best -Abhi On Thu, Oct 16, 2008 at 2:04 PM, Brian Pratt <[EMAIL PROTECTED]>wrote: > At a minimum the interactxsl thing

[spctools-discuss] ReAdW-4.0.2 execution problem

2008-10-17 Thread Carsten
Hi I just installed ReadW ( Xalibur is installed) but when I tried to execute ReadW the command windowe just flashed up and closes again. The same problem occures after starting the xalibur-ddl file. Any suggestions? BW Carsten --~--~-~--~~~---~--~~ You received

[spctools-discuss] Re: no output when running ProteinProphet

2008-10-17 Thread John Lee
Anyone else met this problem? --~--~-~--~~~---~--~~ 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 ema

[spctools-discuss] Re: no output when running ProteinProphet

2008-10-17 Thread John Lee
Anyone else met this problem? --~--~-~--~~~---~--~~ 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 emai