I've been trying to figure out how the deltaMass, number of tryptic
termini, and number of missed cleavages are used to adjust the
discriminate score after the the calculation that you show in your
message. Can you tell me where in the code this takes place?
Thanks,
Bill
On Mar 11, 11:44 am
Here's what the problem was, the fomula is correct but I was using the
constants for the wrong charge state.
the spectra was a +1 but I was using the constants array position 1
instead of 0.
Thanks,
Bill
On Oct 8, 2:21 pm, Natalie Tasman natalie.tas...@insilicos.com
wrote:
Hi Bill,
We build
So, is that an error in the code or is my compiler special, that is,
do I change my local copy or has the trunk been updated?
Thanks,
Bill
On Nov 17, 5:14 pm, Brian Pratt brian.pr...@insilicos.com wrote:
Oops, I wasn't up to date after all, sorry.
Just add an (int) cast in front of that strlen
:\sashimi\trunk
\trans_proteomic_pipeline\src\Parsers\Algorithm2XML\Sequest2XML\Release
\BuildLog.htm
37CombineOut - 1 error(s), 1 warning(s)
The Centos build worked well. The pre-install scripts are very
helpful.
Thanks for your help.
Bill
On Nov 16, 5:40 pm, Brian Pratt brian.pr
but it
would have saved me a lot of time if, at least, the README file had
been updated when the build procedure was changed.
Thanks,
Bill
On Nov 9, 11:59 am, Brian Pratt brian.pr...@insilicos.com wrote:
Can you please guide me to the correct win_lib folder for the trunk or
is it no longer needed
Can you tell me how to extract the external libs manually or how to
troubleshoot the makefile?
Thanks,
Bill
On Nov 16, 1:34 pm, Brian Pratt brian.pr...@insilicos.com wrote:
Bill,
Agreed, it's bad when the docs get stale. I'll update that windows readme.
As to the IDE, I'm with you
.
Can you please guide me to the correct win_lib folder for the trunk or
is it no longer needed?
Thanks,
Bill
On Nov 6, 6:27 pm, Brian Pratt brian.pr...@insilicos.com wrote:
Just about everything links against tpplib, so yes, if that's not happy
nobody's happy. And tpplib depends on zlib, so
Thanks again for your feedback. The printf is a good idea but I have a
new computer and need to get the TPP development environment set up
anyway.
-Bill
On Oct 7, 9:36 am, Brendan brend...@proteinms.net wrote:
Hi Bill,
Depending on how much you hate it, you could also just use some simple
Thanks for your help. My next step was to run it in a debugger but I
don't have a visual studio license. I hate to do it but I guess I'll
have to give Microsoft more money.I'll post the results if I figure it
out.
Bill
On Oct 6, 8:44 am, Brendan brend...@proteinms.net wrote:
Hi Bill,
I think
,
Bill
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This was Fedora but try
yum search perl-devel
yum install if you find it.
On Aug 16, 9:40 pm, GATTACA dfer...@umich.edu wrote:
Hello Bill.
I'm having the same problem on Centos 5.2
I can't find the perl-devel rpm anywhere
Could you tell me where you got it?
I'm running perl 5.8.8 on x86_64
I'm running into the error below when compiling from the svn chekout
of release 4.2
on Fedora core 8
with gcc 4.1.2.
There is a build/linux/tpplib_perl.pm but no tpplib_perl.so.
Has anyone seen anyting like this?
Also, is there a public Amason ec2 image out there anywhere?
Thanks,
Bill
swig -c
It had perl installed but not the header files libraries.
yum install perl-devel has solved this problem.
Still interested in knowing if there is ec2 image out there though.
Thanks,
Bill
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Thanks Brian!
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I'd like to try to reproduce some searches that are posted on Peptide
Atlas. Is it possible to get a copy of the database that was used;
YeastCombNR_20070207_ForwDecoy.fasta?
Thanks,
Bill
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Thanks for your offer. I gladly accept.
I'll try rebuilding with the lines that run ProphetModels.pl and
ProtProphetModels.pl commented out and let you know how it goes.
Bill
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Okay, that worked. I also had to comment out the execution of
PepXMLViewer.cgi.
So, when ProteinProphet finishes it leaves behind a new file:
java.io.IOException: Failed to remove work directory /raid/labkey/Test/
Human Standard/xtandem/test8/UPS1-01.work unexpected files found:
writeScript(OUTFILE, datafile, num_prots);
}
Thanks agian for your quick responses.
Bill
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ditched it due to these kinds of link issues.
You ditched what?
Thanks,
Bill
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added /usr/lib64 to the front of my
LD_LIBRARY_PATH but got the same message. Do you know how I can get ld
to look in lib64 instead of lib?
Thanks,
Bill
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Never mind, I think its okay now. I'm not sure why though?
Thanks again for your help.
Bill
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in the Makefile.config.incld next.
Thanks again,
Bill
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::char_traitschar
]+0x38): undefined reference to `std::basic_streambufchar,
std::char_traitschar ::xsputn(char const*, int)'
collect2: ld returned 1 exit status
make: *** [ProteinProphet] Error 1
Thanks in advance for your help.
Bill
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You received
the problem.
-Original Message-
From: spctools-discuss@googlegroups.com
[mailto:spctools-disc...@googlegroups.com] On Behalf Of bill
Sent: Monday, March 16, 2009 6:46 AM
To: spctools-discuss
Subject: [spctools-discuss] Re: protein prophet can't find protein in
database
Thanks for your
Thanks for your help.
On Mar 13, 4:22 pm, Insilicos brian.pratt.insili...@gmail.com wrote:
Looks like this is a Monday task now... Sorry.
Brian
On Mar 12, 2009, at 2:41 PM, bill nelson...@gmail.com wrote:
much obliged.
It's on its way as kentucky.tar. Not name correctly though I
-zero exit code: 256
QUIT - the job is incomplete
The protein is in the database. The pep.xml entry for the missing
peptide is at about scan 1500. The database is much larger than I have
tried before; the NCBInr database at about 3.5G.
Thanks for any ideas,
Bill
to get more information. Also you can use the
database tools in Bioworks Browser to create indexed databases on your
disk.
Bill
On Feb 21, 9:04 am, David Chiang da...@sagenresearch.com wrote:
FYI - Our company makes the SORCERER 2 integrated data appliance
system with a fast SEQUEST
the mzXML to reflect the
original raw data.
Has anybody had any experience in addressing this issue with wiff to
mgf?
Thanks,
Bill
On Feb 16, 1:13 pm, Matthew Chambers matthew.chamb...@vanderbilt.edu
wrote:
It depends what you want to use the MGF for. I think the TPP pipeline
for the near future
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