Hello, I’ve noticed 2 issues in the recent update of coot (v0.9.8.5 from CCP4i) on an Intel mac updated to Ventura (13.0.1). I did not test on Linux.
When I delete a molecule, my Coot/X11 window « disappears ». It is not closed/killed but somehow minimized. I can get it back from my dock, but a bit annoying. Here’s what the console says. (set-delete-residue-mode) (2) " O5 "/1/chainid="A"/625/FUC, occ: 1.000 with B-factor: 66.076 element: " O" at (26.959,-34.446,11.593) : 0.132 INFO:: backup file name coot-backup/_Users_xbrazzolotto_Desktop_Crystallography_20221116_MR37216_MR-CoX_Phenix_MR372016_20221116_refine_3-coot-1.pdb_Wed_Nov_16_18:30:17_2022_modification_11.pdb.gz (delete-residue 2 "A" 625 "") (clear-pending-delete-item) Pending Picks Cleared (delete-residue-by-atom-index 2 4280 1) debug:: g.safe_scheme_command() with command post-manipulation-hook When I build sugar chains with the N-linked Glycan module, they are not building correctly. It looks like it messes up with the wrong atom for linking. When I try to add an Aplpha1-6 FUC residue to my initial NAG, here is what the console reports ......... checking for /Applications/ccp4-8.0/coot_py2/share/coot/link-by-torsion-to-FUC-core-ALPHA1-6.tab reading /Applications/ccp4-8.0/coot_py2/share/coot/link-by-torsion-to-FUC-core-ALPHA1-6.tab reading /Applications/ccp4-8.0/coot_py2/share/coot/FUC-decorations.tab INFO:: backup file name coot-backup/_Users_xbrazzolotto_Desktop_Crystallography_20221116_MR37216_MR-CoX_Phenix_MR372016_20221116_refine_3-coot-1.pdb_Wed_Nov_16_18:30:17_2022_modification_13.pdb.gz WARNING:: Dictionary links atom not found in link residues link # 0 is pyranose ring torsion # PASS link # 1 has residues [spec: 1 "A" 625 ""] [spec: 1 "A" 625 ""] [spec: 1 "A" 624 ""] [spec: 1 "A" 624 ""] link # 1 has link_atoms: [spec: model 1 "A" 625 "" " C6 " ""] [spec: model -1 "unset" -2147483647 "" "" ""] [spec: model 1 "A" 624 "" " C1 " ""] [spec: model 1 "A" 624 "" " C2 " ""] link # 2 has residues [spec: 1 "A" 625 ""] [spec: 1 "A" 625 ""] [spec: 1 "A" 625 ""] [spec: 1 "A" 624 ""] link # 2 has link_atoms: [spec: model 1 "A" 625 "" " C5 " ""] [spec: model 1 "A" 625 "" " C6 " ""] [spec: model -1 "unset" -2147483647 "" "" ""] [spec: model 1 "A" 624 "" " C1 " ""] INFO:: backup file name coot-backup/_Users_xbrazzolotto_Desktop_Crystallography_20221116_MR37216_MR-CoX_Phenix_MR372016_20221116_refine_3-coot-1.pdb_Wed_Nov_16_18:30:17_2022_modification_14.pdb.gz INFO:: replace_coords: 24 atoms updated. model file does not exist "/Users/jenkins/workspace/CCP4/coot-py2-osx-clang/devtools/install/share/coot/data/cho-models/model-level-2-FUC-BETA1-6-NAG.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 32 atoms debug:: on creation last_restraints is 0x7fdabbc51800 INFO:: from_res_vec() created 107 monomer restraints created 31 bond restraints created 41 angle restraints created 8 plane restraints created 9 chiral vol restraints created 0 improper dihedral restraints created 18 torsion restraints Made 0 link bond restraints Made 0 link angle restraints Made 0 link plane restraints Made 0 link trans-peptide restraints Made 1 CHO-SS-and-other bond restraints Made 3 CHO-SS-and-other angle restraints Made 1 CHO-SS-and-other plane restraints Made 0 CHO-SS-and-other trans-peptide restraints INFO:: added 0 helical restraints INFO:: Model: Bad Bond: [spec: model 1 "A" 625 "" " C5 " ""] to [spec: model 1 "A" 625 "" " O5 " ""] nZ 3.14 delta -0.031 target 1.445 sigma 0.010 distortion 9.872 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 624 "" " O6 " ""] NAG to [spec: model 1 "A" 625 "" " C1 " ""] FUC delta -2.316 target 3.710 distortion 1011013.562 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 625 "" " C3 " ""] FUC to [spec: model 1 "A" 14 "" " CD " ""] ARG delta -2.043 target 4.110 distortion 30079.891 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 625 "" " C4 " ""] FUC to [spec: model 1 "A" 14 "" " NE " ""] ARG delta -1.857 target 3.790 distortion 25321.238 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 625 "" " C3 " ""] FUC to [spec: model 1 "A" 14 "" " NE " ""] ARG delta -1.797 target 3.790 distortion 17521.352 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 625 "" " C4 " ""] FUC to [spec: model 1 "A" 14 "" " CZ " ""] ARG delta -1.776 target 3.940 distortion 10307.841 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 624 "" " C6 " ""] NAG to [spec: model 1 "A" 625 "" " C1 " ""] FUC delta -1.770 target 4.110 distortion 6656.417 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 625 "" " C5 " ""] FUC to [spec: model 1 "A" 14 "" " CZ " ""] ARG delta -1.513 target 3.940 distortion 2529.084 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 625 "" " C6 " ""] FUC to [spec: model 1 "A" 14 "" " NH2" ""] ARG delta -1.450 target 3.780 distortion 2507.471 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 625 "" " O3 " ""] FUC to [spec: model 1 "A" 14 "" " CD " ""] ARG delta -1.401 target 3.680 distortion 2369.297 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 625 "" " C4 " ""] FUC to [spec: model 1 "A" 14 "" " NH2" ""] ARG delta -1.405 target 3.790 distortion 1950.454 Minimum found (iteration number 8) at -846.214 Final Estimated RMS Z Scores: bonds: 0.380 angles: 0.955 improper-dihedrals: N/A torsions: 0.627 trans-peptide: N/A planes: 1.277 from 13 restraints parallel planes: N/A non-bonded: -0.417 chiral vol: 1.228 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A -------- Results --------- INFO:: Model: Bad Chiral Volume: [spec: model 1 "A" 57 "" " CA " ""] delta -0.365 target 2.541 sigma 0.100 distortion 13.332 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 57 "" " O " ""] ASN to [spec: model 1 "A" 59 "" " CG2" ""] THR delta -0.859 target 3.700 distortion 151.441 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 57 "" " O " ""] ASN to [spec: model 1 "A" 14 "" " O " ""] ARG delta -0.602 target 3.280 distortion 64.018 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 57 "" " N " ""] ASN to [spec: model 1 "A" 56 "" " CD1" ""] TRP delta -0.557 target 3.580 distortion 38.754 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 57 "" " OD1" ""] ASN to [spec: model 1 "A" 14 "" " NH1" ""] ARG delta -0.411 target 2.880 distortion 30.485 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 624 "" " C6 " ""] NAG to [spec: model 1 "A" 625 "" " C1 " ""] FUC delta -0.512 target 4.110 distortion 21.697 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 624 "" " O4 " ""] NAG to [spec: model 1 "A" 625 "" " C6 " ""] FUC delta -0.398 target 3.700 distortion 15.499 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 625 "" " C6 " ""] FUC to [spec: model 1 "A" 14 "" " CZ " ""] ARG delta -0.412 target 3.930 distortion 14.601 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 57 "" " CG " ""] ASN to [spec: model 1 "A" 14 "" " NH1" ""] ARG delta -0.351 target 3.590 distortion 12.615 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 624 "" " C1 " ""] NAG to [spec: model 1 "A" 624 "" " C8 " ""] NAG delta -0.399 target 4.130 distortion 12.328 INFO:: Model: Bad Non-Bonded Contact: [spec: model 1 "A" 57 "" " N " ""] ASN to [spec: model 1 "A" 56 "" " CG " ""] TRP delta -0.333 target 3.580 distortion 11.400 Final Estimated RMS Z Scores bonds: 0.380 angles: 0.955 improper-dihedrals: N/A torsions: 0.627 trans-peptide: N/A planes: 1.277 from 13 restraints parallel planes: N/A non-bonded: -0.417 chiral vol: 1.228 rama plot: N/A start_pos: N/A TargetPos: N/A GemanMcCl: N/A INFO:: backup file name coot-backup/_Users_xbrazzolotto_Desktop_Crystallography_20221116_MR37216_MR-CoX_Phenix_MR372016_20221116_refine_3-coot-1.pdb_Wed_Nov_16_18:30:17_2022_modification_15.pdb.gz INFO:: replace_coords: 32 atoms updated. debug:: in clear_all_atom_pull_restraints() 0 debug:: g.safe_scheme_command() with command post-manipulation-hook In this case the FUC residue is quite far from the NAG residue upon refinement Hope it could help Best Xavier ######################################################################## 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/