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Dear Matthew,
Sorry to hear that you are having trouble with mrbump. From the log you
sent us it does look as if it is a firewall problem. Do you need to access
a proxy server to get connections to the outside? If so, you may need to
set the http_proxy environment variable in the shell from where you are
running ccp4i/mrbump.
Kind regards,
Ronan
#########################################################################
Ronan Keegan email: [EMAIL PROTECTED]
e-HTPX/CCP4 phone: (+)44-1925-603701
C18, Daresbury Laboratory fax: (+)44-1925-603825
Warrington WA4 4AD
UK
#########################################################################
On Fri, 18 Aug 2006, Matthew Wilce wrote:
> Dear CCP4,
> when trying to run mrbump I get the errors pasted below.
>
> I am running CCP4 V6.0 under OSX (intel) and have just installed the
> lastest mrbump.
>
> Could these errors be caused by the firewall at my institution? Is
> there a way around this?
>
> Thanks in advance,
> Matt
>
>
>
> Database update: Checking the web to see if newer versions of the
> search databases exist.
> ************************************************************************
> ***
> * Information from CCP4Interface script
> ************************************************************************
> ***
> The program run with command: python -u /sw/share/xtal/ccp4-6.0/bin/
> mrbump HKLIN /Volumes/G2F8/est/data/master1.mtz SEQIN /Volumes/G2F8/
> est/phasing/est.pir HKLOUT /Volumes/G2
> F8/est/mrbump/master1_mrbump_soln1.mtz XYZOUT /Volumes/G2F8/est/
> mrbump/master1_mrbump_soln1.pdb
> has failed with error message
> Traceback (most recent call last):
> File "/sw/share/xtal/ccp4-6.0/bin/mrbump", line 49, in ?
> init.mrbump_initialisation(sys.argv)
> File "/sw/share/xtal/ccp4-6.0/src/mrbump/include/initialisation/
> MRBUMP_initialise.py", line 232, in mrbump_initialisation
> self.db_tools.test_databases(self.environment,
> self.keywords.UPDATE)
> File "/sw/share/xtal/ccp4-6.0/src/mrbump/include/initialisation/
> MRBUMP_update_DB.py", line 68, in test_databases
> self.update_DB('Fasta DB', 'http://www.ccp4.ac.uk/ronan/bmp_data/
> pdb_ATOMseqs.txt', environment.SETUP_DIR + '/pdb_ATOMseqs.txt')
> File "/sw/share/xtal/ccp4-6.0/src/mrbump/include/initialisation/
> MRBUMP_update_DB.py", line 84, in update_DB
> u=urllib.urlopen(url)
> File "/sw/lib/python2.4/urllib.py", line 77, in urlopen
> return opener.open(url)
> File "/sw/lib/python2.4/urllib.py", line 185, in open
> return getattr(self, name)(url)
> File "/sw/lib/python2.4/urllib.py", line 308, in open_http
> h.endheaders()
> File "/sw/lib/python2.4/httplib.py", line 795, in endheaders
> self._send_output()
> File "/sw/lib/python2.4/httplib.py", line 676, in _send_output
> self.send(msg)
> File "/sw/lib/python2.4/httplib.py", line 643, in send
> self.connect()
> File "/sw/lib/python2.4/httplib.py", line 611, in connect
> socket.SOCK_STREAM):
> IOError: [Errno socket error] (7, 'No address associated with nodename')
> ************************************************************************
> ***
>
>
>
> Associate Professor Matthew Wilce
> Department of Biochemistry and Molecular Biology
> Monash University
> Victoria, Australia
>
> Phone: 613 9905 1086
>
>
>
>
