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
It seems very similar to Taka's issue where if I add an NAG using the Carbohydrate module, I get my NAG, but no link. I only recently updated to 0.9.8.6 (dont remember what version I was using before), but there were no problems then. Attaching the terminal output below. Looks like the NAG-ASN links and files are missing?? INFO:: using standard CCP4 Refmac dictionary to search for "NAG" There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/n/NAG.cif 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 WARNING:: Link not found in dictionary WARNING:: Neither index2 15 nor index3 14 has forward atoms! INFO:: replace_coords: 22 atoms updated. model file does not exist "/Users/jenkins/workspace/CCP4/coot-py2-osx-clang/devtools/install/share/coot/data/cho-models/model-level-1-NAG-NAG-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 38 atoms debug:: on creation last_restraints is 0x7fb326b64200 INFO:: from_res_vec() created 108 monomer restraints created 35 bond restraints created 43 angle restraints created 5 plane restraints created 8 chiral vol restraints created 0 improper dihedral restraints created 17 torsion restraints Made 2 link bond restraints Made 6 link angle restraints Made 4 link plane restraints Made 0 link trans-peptide restraints link type "NAG-ASN" not found in dictionary!! ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
