Hi,
We have been calculating structures with oleic acid as a ligand and have
an issue with importing the structures back into analysis:
When importing the structures via the Structure->Structures popup
(ccpnmr/analysis/popups/EditStructures.py importStructure) we see an
errror such as:
Cannot find ChemComp XML file carbohydrate, OLA
Cannot find ChemComp XML file other, OLA
I think I understand why this is (line numbers etc refer to updated 2.1.5)
-
The chain of events from importStructure looks like
analysis.core.StructureBasic getStructureFromFile
calls
analysis.core.StructureBasic makeStructureDictFromRoughPdb
reads the PDB into a dictionary with the three letter residue code from
the PDB file stored as resName
now getStructureFromFile calls
analysis.core.StructureBasic makeStructures
passing it the dictionary created by makeStructureDictFromRoughPdb
which at line 1157 calls
analysis.core.StructureBasic getBestChemComp
passing it the resName - the will have the SAME CASE as in the PDB file
Now getBestChemComp does some case changing magic at line 874 for
'protein' but not for 'other' so when our OLA falls through to
ccp.general.Io getChemComp
it searches for a file matching "OLA" rather than "Ola"
and fails to find one anywhere with the errors being displayed from line
442 of ccp.general.Io.py
SOLUTION?: It looks to me as if most ccpCodes are Ull format so need the
same type of magic that happens to protein residues. It seems to me that
the lower() trick should be safe to use on all ccpCodes since it should
not affect ccpCodes that contain digits. Any chance of a quick fix?
Aside: the carbohydrate thing puzzled me for a while, but Ola (and many
other fatty acid type things) satisfy the guess for type carbohydrate in
analysis.core.StructureBasic getBestMolType. No biggy.
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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