[BiO BB] Re: Gene ontology PDB files & InterproScan query

Dr Nicky Mulder nmulder at science.uct.ac.za
Thu Nov 16 12:28:32 EST 2006

>Message: 3
>Date: Tue, 14 Nov 2006 12:32:36 -0600
>From: kannaiah at bsd.uchicago.edu
>Subject: [BiO BB] InterProscan XML output error
>To: bio_bulletin_board at bioinformatics.org
>Message-ID: <1163529156.455a0bc409e46 at netmail.bsd.uchicago.edu>
>Content-Type: text/plain; charset=ISO-8859-1
>Anybody here use Interproscan anytime?
>If so, I am wondering if you ever ran into an error like this: An xml output error.
>Not sure whats going wrong here:(. Any ideas?
>Thank you.
>[root at cccluster iprscan]# /clusta/shah/local_progs/iprscan/bin/iprscan -cli
>-appl hmmsmart -appl hmmpfam -i /clusta/shah/local_progs/iprscan/test.seq -o
>SUBMITTED iprscan-20061114-12101842
>        Iprscan job iprscan-20061114-12101842 failed and exit with status code 256
>unavailable : No such file or directory
>/clusta/shah/local_progs/iprscan/bin/iprscan_wrapper.pl: failed to send error to
>administrator: no destination address
>Tool:  iprscan
>JobID: iprscan-20061114-12101842
>Time:  Tue Nov 14 12:11:37 2006
>supervise: doRawResults: failed to create XML output :
>Job submission parameters:
>DD              14
>MM              11
>YYYY            2006
>appl            hmmsmart,hmmpfam
>cmd             submit
>crc             1
>format          xml
>frame           6
>hh              12
>jobid           iprscan-20061114-12101842
>mm              10
>nseqs           3
>onego           1
>remotehost      cccluster.uchicago.cc
>seq.1.1.crc64   F94D07049A6D489D
>seq.1.1.id      RS16_ECOLI
>seq.1.1.len     82
>seq.1.2.crc64   D44DAE8C544CB7C1
>seq.1.2.id      Q9RHD9
>seq.1.2.len     267
>seq.1.3.crc64   CD84A335CCFFE6D7
>seq.1.3.id      Y902_MYCTU
>seq.1.3.len     446
>seqtype         P
>srchtype        interactive
>ss              18
>submission      cli
>tool            iprscan
>NOTE: the newlines have been replaced with backslash.
You should send this query direclty to interhelp at ebi.ac.uk, who can help.

>Message: 4
>Date: Wed, 15 Nov 2006 12:41:13 +0000 (GMT)
>From: Ulisses Dias <ulimard at yahoo.com.br>
>Subject: [BiO BB] Gene ontology PDB files
>To: "General Forum at Bioinformatics.Org"
>	<bio_bulletin_board at bioinformatics.org>
>Message-ID: <20061115124114.10256.qmail at web56613.mail.re3.yahoo.com>
>Content-Type: text/plain; charset=iso-8859-1
>   Anyone knows how can I get the PDB numbers for all the genes products associated to a GO term?
>Thank you
>  Ulisses Dias
The GOA database provides a file of PDB to GO annotations, see this page 
of downloades:

See the readme file for more info on the PDB GO annotations

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