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
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