Hi Paul, trying to insert an alpha1-6 L-fucose (Glyco->Add N-linked Glycan->Add an ALPHA1-6 FUC) in Coot 0.9.8.95 gives a complaint about a missing model file "model-level-2-FUC-ALPHA1-6-NAG.tab"
There is no such file in coot-gtk2-python/share/coot/data/cho-models/ nor in coot-Linux-GenuineIntel---gtk2-python/share/coot/data/cho-models/ I cannot find one on GitHub either: https://github.com/pemsley/coot/tree/main/data/cho-models There is a model-level-2-FUC-BETA1-6-NAG.tab, however. Coot still inserts a fucose (but far away from its NAG friend) and tries to refine the tree, but fails miserably. The fucose ends up lonely and disconnected from the carbohydrate tree it was supposed to connect to. With best regards, Markus Log: Invariant Violation debug:: g.safe_scheme_command() with command post-set-rotation-centre-hook There are 2 data in /software/share/coot-0.9.8.95/coot-gtk2-python/share/coot/data/cho-acedrg/NAG-acedrg.cif Read 30 atoms/links in restraints from /software/share/coot-0.9.8.95/coot-gtk2-python/share/coot/data/cho-acedrg/NAG-acedrg.cif There are 2 data in /software/share/coot-0.9.8.95/coot-gtk2-python/share/coot/data/cho-acedrg/MAN-acedrg.cif Read 24 atoms/links in restraints from /software/share/coot-0.9.8.95/coot-gtk2-python/share/coot/data/cho-acedrg/MAN-acedrg.cif There are 2 data in /software/share/coot-0.9.8.95/coot-gtk2-python/share/coot/data/cho-acedrg/BMA-acedrg.cif Read 24 atoms/links in restraints from /software/share/coot-0.9.8.95/coot-gtk2-python/share/coot/data/cho-acedrg/BMA-acedrg.cif There are 2 data in /software/share/coot-0.9.8.95/coot-gtk2-python/share/coot/data/cho-acedrg/SIA-acedrg.cif Read 39 atoms/links in restraints from /software/share/coot-0.9.8.95/coot-gtk2-python/share/coot/data/cho-acedrg/SIA-acedrg.cif There are 2 data in /software/share/coot-0.9.8.95/coot-gtk2-python/share/coot/data/cho-acedrg/FUC-acedrg.cif Read 23 atoms/links in restraints from /software/share/coot-0.9.8.95/coot-gtk2-python/share/coot/data/cho-acedrg/FUC-acedrg.cif There are 2 data in /software/share/coot-0.9.8.95/coot-gtk2-python/share/coot/data/cho-acedrg/XYP-acedrg.cif Read 20 atoms/links in restraints from /software/share/coot-0.9.8.95/coot-gtk2-python/share/coot/data/cho-acedrg/XYP-acedrg.cif There are 2 data in /software/share/coot-0.9.8.95/coot-Linux-GenuineIntel---gtk2-python/share/coot/lib/data/monomers/g/GAL.cif There are 2 data in /software/share/coot-0.9.8.95/coot-Linux-GenuineIntel---gtk2-python/share/coot/lib/data/monomers/g/GLC.cif There are 2 data in /software/share/coot-0.9.8.95/coot-Linux-GenuineIntel---gtk2-python/share/coot/lib/data/monomers/b/BGC.cif find_rooted_tree returns tree: ASN [spec: 1 "A" 133 ""] pyr-ASN NAG [spec: 1 "A" 459 ""] BETA1-4 NAG [spec: 1 "A" 460 ""] BETA1-4 BMA [spec: 1 "A" 461 ""] BETA1-6 MAN [spec: 1 "A" 462 ""] ALPHA1-3 MAN [spec: 1 "A" 463 ""] find_rooted_tree returns tree: ASN [spec: 1 "A" 133 ""] pyr-ASN NAG [spec: 1 "A" 459 ""] BETA1-4 NAG [spec: 1 "A" 460 ""] BETA1-4 BMA [spec: 1 "A" 461 ""] BETA1-6 MAN [spec: 1 "A" 462 ""] ALPHA1-3 MAN [spec: 1 "A" 463 ""] find_rooted_tree returns tree: ASN [spec: 1 "A" 133 ""] pyr-ASN NAG [spec: 1 "A" 459 ""] BETA1-4 NAG [spec: 1 "A" 460 ""] BETA1-4 BMA [spec: 1 "A" 461 ""] BETA1-6 MAN [spec: 1 "A" 462 ""] ALPHA1-3 MAN [spec: 1 "A" 463 ""] ......... checking for /software/share/coot-0.9.8.95/coot-Linux-GenuineIntel---gtk2-python/share/coot/link-by-torsion-to-FUC-core-ALPHA1-6.tab reading /software/share/coot-0.9.8.95/coot-Linux-GenuineIntel---gtk2-python/share/coot/link-by-torsion-to-FUC-core-ALPHA1-6.tab reading /software/share/coot-0.9.8.95/coot-Linux-GenuineIntel---gtk2-python/share/coot/FUC-decorations.tab link_type_filter_general() for pyr-ASN link_type_filter_general() checking type pyr-ASN and returns "" link_type_filter_general() for pyr-ASN link_type_filter_general() checking type pyr-ASN and returns "pyr-ASN" link_type_filter_general() for BETA1-4 link_type_filter_general() checking type BETA1-4 and returns "BETA1-4" link_type_filter_general() for ALPHA1-2 link_type_filter_general() checking type ALPHA1-2 and returns "" link_type_filter_general() for ALPHA1-2 link_type_filter_general() checking type ALPHA1-2 and returns "" INFO:: replace_coords: 24 atoms updated. find_rooted_tree returns tree: ASN [spec: 1 "A" 133 ""] pyr-ASN NAG [spec: 1 "A" 459 ""] BETA1-4 NAG [spec: 1 "A" 460 ""] BETA1-4 BMA [spec: 1 "A" 461 ""] BETA1-6 MAN [spec: 1 "A" 462 ""] ALPHA1-3 MAN [spec: 1 "A" 463 ""] ALPHA1-6 FUC [spec: 1 "A" 475 ""] model file does not exist "/software/share/coot-0.9.8.95/coot-gtk2-python/share/coot/data/cho-models/model-level-2-FUC-ALPHA1-6-NAG.tab" ----------------- in create_mmdbmanager_from_res_vector() alt_conf is "" ----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0"" -- Markus Meier, Ph.D. Research Associate University of Manitoba Department of Chemistry 144 Dysart Road Winnipeg, MB, R3T 2N2, Canada Phone: +1 204 474 7172 E-mail: markus.me...@umanitoba.ca ######################################################################## 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/
