On Fri, 7 Nov 2014, Brian Smith wrote:
> These changes in that file seem to work for accessing ccpforge:
>
> #ccpForgeUrl =
> "http://ccpforge.cse.rl.ac.uk/gf/project/ccpn-chemcomp/scmcvs/?action=browse&root=ccpn-chemcomp&pathrev=MAIN&path=/"
> ccpForgeUrl =
> "http://ccpforge.cse.rl.ac.uk/gf/project/ccpn-chemcomp/scmcvs/?action=browse&path="
> #checkOutDir = "~checkout~"
> checkOutDir = ""
Not quite right - this results in downloading the web page rather than the
xml. It's as simple as chaning the ~ to # in the chechOutDir ! So keep
the original ccpForgeUrl definition and then
checkOutDir = "*checkout*"
> But I'm still getting
>
> Cannot find file:
> Cannot find ChemComp XML file carbohydrate, OLA.
> Cannot find file:
> Cannot find ChemComp XML file other, OLA.
>
> Which I think relates to getBestChemComp() that used to be in
> ccpnmr/analysis/core/StructureBasic.py but is now in
> ccp/lib/DataConvert.Lib.py where I see that it should be testing with the Xxx
> version of the ChemComp name also, but does not seem to (since it should find
> Ola in other above.
This is due to the function findCcpForgeDownloadLink() in
ccp/general/Io.py which does
if ccpCode == tmpCcpCode:
but ccpCode seems to be upper case OLA whereas the ones harvested from the
archive are Xxx. The CcpCode should be Ola so I guess the three letter
code is not getting translated as the incoming PDB is parsed?
If I force the issue by defining
ccpCode = "Ola";
before the comparison, then I get the right file downloaded (and then
another error - boohoo).
> In fact, the ccpforge access issue should be a red herring since I already
> have the chemComp in the project!
Still not clear why the copies of this chemComp file in the project itself
and in the analysis installation are not used. Maybe my new error is about
the fact that the chemComp is already loaded into memory:
Downloaded ChemComp other, OLA from server
http://ccpforge.cse.rl.ac.uk/gf/project/ccpn-chemcomp/scmcvs/?action=browse&root=ccpn-chemcomp&pathrev=MAIN&path=*checkout*/ccpn-chemcomp/data/pdbe/chemComp/archive/ChemComp/other/O,
written to file
/home/marinai/structures/Asp18/20131120/As_p18/ccp/molecule/ChemComp/other+Ola+msd_ccpnRef_2007-12-11-10-18-16_00004.xml!
Error loading file for: <ccp.molecule.ChemComp.NonStdChemComp ['other',
'Ola']>
Reading: <open file
'/home/marinai/structures/Asp18/20131120/As_p18/ccp/molecule/ChemComp/other+Ola+msd_ccpnRef_2007-12-11-10-18-16_00004.xml',
mode 'r' at 0x328cd780>
Last xml tag read: CHEM.NonStdChemComp
Parser state was: reading
Object stack was empty
--
Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
College of Medical, Veterinary & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089 Fax: 0141 330 4600
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