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 N to 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 C7 to B 273 OD1 #### glyco close: 1.522 B 1129 O7 to B 273 CG #### 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" 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" ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" returning an atom selection for all moving atoms 35 atoms debug:: on creation last_restraints is 0x7fa3e8bd4600 INFO:: from_res_vec() created 98 monomer restraints created 32 bond restraints created 38 angle restraints created 6 plane restraints created 6 chiral vol restraints created 0 improper dihedral restraints created 16 torsion restraints Made 2 link bond restraints Made 6 link angle restraints Made 4 link plane restraints Made 2 link trans-peptide restraints DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 1 #### glyco close: 1.927 B 272 CB to B 1129 C8 debug:: find_glycosidic_linkage_type() for B 272 GLN,B 1129 NAG returns "" DEBUG:: find_glycosidic_linkage_type() number of sorted distances: 1 #### glyco close: 1.927 B 1129 C8 to B 272 CB debug:: find_glycosidic_linkage_type() for B 1129 NAG,B 272 GLN returns "" 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 N to 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 C7 to B 273 OD1 #### glyco close: 1.522 B 1129 O7 to B 273 CG #### 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" -- Kelvin Lau Protein production and structure core facility - PTPSP EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: kelvin....@epfl.ch<mailto:kelvin....@epfl.ch> Phone: +41 21 69 34494 On 3 Jan 2023, at 10:27, Lau Kelvin <00005aaf8435dbef-dmarc-requ...@jiscmail.ac.uk<mailto:00005aaf8435dbef-dmarc-requ...@jiscmail.ac.uk>> wrote: Thank you Paul! Ill give it a spin when the ccp4 distribution updates it as well. -- Kelvin Lau Protein production and structure core facility - PTPSP EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: kelvin....@epfl.ch<mailto:kelvin....@epfl.ch> Phone: +41 21 69 34494 On 3 Jan 2023, at 01:03, Paul Emsley <pems...@mrc-lmb.cam.ac.uk<mailto:pems...@mrc-lmb.cam.ac.uk>> wrote: On 27/12/2022 18:59, Kelvin Lau wrote: Dear Paul I looked back the forum and similar to Taka's issue in 0.9.8.4 I am also experience it with both Coot 0.9.8.6 EL (ccp4 build) and 0.9.8.5 (ccpEM) build. MacOS 12.6.1 Hello Kelvin, I believe that this issue is fixed in 0.9.8.7. 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