Dear Paul
I got around to updating via ccp4.
In 0.9.8.7 EL I can add the glycans like before, but I do not see a link. The
glyco module also no longer recognises that there is a glycan present at the
Asn, so when I add another NAG, they just overlap.
Seems like it can’t find :
. checking for
/Applications/ccp4-8.0/coot_py2/share/coot/link-by-torsion-to-NAG-core-NAG-ASN.tab
..that failed - trying
/Applications/ccp4-8.0/coot_py2/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab
reading
/Applications/ccp4-8.0/coot_py2/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab
reading /Applications/ccp4-8.0/coot_py2/share/coot/NAG-decorations.tab
INFO:: backup file name
coot-backup/Documents_Facility_EM_XXX_real_space_refined_006-coot-0.pdb_Wed_Jan_18_09:45:09_2023_modification_0.pdb.gz
WARNING:: Link not found in dictionary
debug:: find_glycosidic_linkage_type() for B 1129 NAG,B 273 ASN returns
"pyr-ASN"
model file does not exist
"/Users/jenkins/workspace/CCP4/coot-py2-osx-clang/devtools/install/share/coot/data/cho-models/model-level-1-NAG-pyr-ASN-ASN.tab"
Here is the output
(0) " CG "/1/chainid="B"/273/ASN, occ: 1 with B-factor: 90.96 element: " C" at
(246.9,215.5,209.6) : 0.1443
INFO:: recentre: clicked on imol: 0
debug:: g.safe_scheme_command() with command post-set-rotation-centre-hook
INFO:: using standard CCP4 Refmac dictionary to search for "BMA"
There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/b/BMA.cif
INFO:: using standard CCP4 Refmac dictionary to search for "MAN"
There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/m/MAN.cif
INFO:: using standard CCP4 Refmac dictionary to search for "GAL"
There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/g/GAL.cif
INFO:: using standard CCP4 Refmac dictionary to search for "GLC"
There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/g/GLC.cif
INFO:: using standard CCP4 Refmac dictionary to search for "FUC"
There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/f/FUC.cif
INFO:: using standard CCP4 Refmac dictionary to search for "XYP"
There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/x/XYP.cif
INFO:: using standard CCP4 Refmac dictionary to search for "BGC"
There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/b/BGC.cif
. checking for
/Applications/ccp4-8.0/coot_py2/share/coot/link-by-torsion-to-NAG-core-NAG-ASN.tab
..that failed - trying
/Applications/ccp4-8.0/coot_py2/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab
reading
/Applications/ccp4-8.0/coot_py2/share/coot/link-by-torsion-to-pyranose-core-NAG-ASN.tab
reading /Applications/ccp4-8.0/coot_py2/share/coot/NAG-decorations.tab
INFO:: backup file name
coot-backup/Documents_Facility_EM_XXX_real_space_refined_006-coot-0.pdb_Wed_Jan_18_09:45:09_2023_modification_0.pdb.gz
WARNING:: Link not found in dictionary
DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 3
glyco close: 2.386 B 273 ND2 to B 1129 O5
glyco close: 2.355 B 273 ND2 to B 1129 C2
glyco close: 1.434 B 273 ND2 to B 1129 C1
debug:: find_glycosidic_linkage_type() for B 273 ASN,B 1129 NAG returns ""
DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 3
glyco close: 2.386 B 1129 O5 to B 273 ND2
glyco close: 2.355 B 1129 C2 to B 273 ND2
glyco close: 1.434 B 1129 C1 to B 273 ND2
debug:: find_glycosidic_linkage_type() for B 1129 NAG,B 273 ASN returns
"pyr-ASN"
INFO:: link torsion generated from link bond restraint
contact_info() constructor added link bond contact 8 7
INFO:: backup file name
coot-backup/Documents_Facility_EM_XXX_real_space_refined_006-coot-0.pdb_Wed_Jan_18_09:45:09_2023_modification_1.pdb.gz
INFO:: replace_coords: 22 atoms updated.
DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 11
glyco close: 2.386 B 273 ND2 to B 1129 O5
glyco close: 2.355 B 273 ND2 to B 1129 C2
glyco close: 2.264 B 273 OD1 to B 1129 N2
glyco close: 2.206 B 273 ND2 to B 1129 O7
glyco close: 2.164 B 273 CG to B 1129 C7
glyco close: 2.158 B 273 Nto B 1129 O7
glyco close: 2.042 B 273 CB to B 1129 O7
glyco close: 1.861 B 273 OD1 to B 1129 O7
glyco close: 1.769 B 273 OD1 to B 1129 C7
glyco close: 1.522 B 273 CG to B 1129 O7
glyco close: 1.434 B 273 ND2 to B 1129 C1
debug:: find_glycosidic_linkage_type() for B 273 ASN,B 1129 NAG returns ""
DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 11
glyco close: 2.386 B 1129 O5 to B 273 ND2
glyco close: 2.355 B 1129 C2 to B 273 ND2
glyco close: 2.264 B 1129 N2 to B 273 OD1
glyco close: 2.206 B 1129 O7 to B 273 ND2
glyco close: 2.164 B 1129 C7 to B 273 CG
glyco close: 2.158 B 1129 O7 to B 273 N
glyco close: 2.042 B 1129 O7 to B 273 CB
glyco close: 1.861 B 1129 O7 to B 273 OD1
glyco close: 1.769 B 1129
