id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3500 Problem simulating glycans mar2294@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 0.93 (2020-04-03) Description When initial global minimization is run, isolde fails with an asserionerror related to the glycans, which were added in COOT 0.8.9.2. Log: UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open2 D:/Research/SARS- > CoV-2/2-43/n20jun29a_maps/spike_2-43_consensus_sharp.mrc Opened spike_2-43_consensus_sharp.mrc, grid size 384,384,384, pixel 1.06, shown at level 0.068, step 2, values float32 > open2 D:/Research/SARS-CoV-2/2-43/model_building/rbd_2-43/rbd_2-43_three.pdb Summary of feedback from opening <_io.textiowrapper name=""D:/Research/SARS- CoV-2/2-43/model_building/rbd_2-43/rbd_2-43_three.pdb"" mode=""rt"" encoding=""utf-8""> --- warning | Ignored bad PDB record found on line 23455 END Chain information for rbd_2-43_three.pdb #2 --- Chain | Description A B C | No description available F H J | No description available G K L | No description available > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > select H 9264 atoms, 1 model selected > delete atoms sel > delete bonds sel > addh Summary of feedback from adding hydrogens to rbd_2-43_three.pdb #2 --- warnings | Not adding hydrogens to /A TYR 369 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A SER 371 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ARG 403 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A GLU 406 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ARG 408 CB because it is missing heavy-atom bond partners 76 messages similar to the above omitted notes | No usable SEQRES records for rbd_2-43_three.pdb (#2) chain A; guessing termini instead No usable SEQRES records for rbd_2-43_three.pdb (#2) chain B; guessing termini instead No usable SEQRES records for rbd_2-43_three.pdb (#2) chain C; guessing termini instead No usable SEQRES records for rbd_2-43_three.pdb (#2) chain F; guessing termini instead No usable SEQRES records for rbd_2-43_three.pdb (#2) chain G; guessing termini instead 4 messages similar to the above omitted Chain-initial residues that are actual N termini: /A PHE 329, /B PHE 329, /C PHE 329, /F GLN 1, /G GLN 1, /H GLN 1, /J GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A THR 531, /B THR 531, /C THR 531, /F SER 129, /G LEU 110, /H SER 129, /J SER 129, /K LEU 110, /L LEU 110 1125 hydrogen bonds /A THR 531 is not terminus, removing H atom from 'C' /B THR 531 is not terminus, removing H atom from 'C' /C THR 531 is not terminus, removing H atom from 'C' /F SER 129 is not terminus, removing H atom from 'C' /G LEU 110 is not terminus, removing H atom from 'C' 4 messages similar to the above omitted 9437 hydrogens added > hide HC > preset cartoons/nucleotides ribbons/slabs Changed 19204 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > isolde start > set selectionWidth 4 Chain information for rbd_2-43_three.pdb --- Chain | Description 2.2/A 2.2/B 2.2/C | No description available 2.2/F 2.2/H 2.2/J | No description available 2.2/G 2.2/K 2.2/L | No description available Done loading forcefield > select #2 19559 atoms, 19833 bonds, 12 models selected No template found for residue A343 (ASN) Adding hydrogens Summary of feedback from adding hydrogens to rbd_2-43_three.pdb #2.2 --- warnings | Not adding hydrogens to /A TYR 369 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A SER 371 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ARG 403 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A GLU 406 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ARG 408 CB because it is missing heavy-atom bond partners 76 messages similar to the above omitted notes | No usable SEQRES records for rbd_2-43_three.pdb (#2.2) chain A; guessing termini instead No usable SEQRES records for rbd_2-43_three.pdb (#2.2) chain B; guessing termini instead No usable SEQRES records for rbd_2-43_three.pdb (#2.2) chain C; guessing termini instead No usable SEQRES records for rbd_2-43_three.pdb (#2.2) chain F; guessing termini instead No usable SEQRES records for rbd_2-43_three.pdb (#2.2) chain G; guessing termini instead 4 messages similar to the above omitted Chain-initial residues that are actual N termini: /A PHE 329, /B PHE 329, /C PHE 329, /F GLN 1, /G GLN 1, /H GLN 1, /J GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A THR 531, /B THR 531, /C THR 531, /F SER 129, /G LEU 110, /H SER 129, /J SER 129, /K LEU 110, /L LEU 110 1061 hydrogen bonds /A THR 531 is not terminus, removing H atom from 'C' /B THR 531 is not terminus, removing H atom from 'C' /C THR 531 is not terminus, removing H atom from 'C' /F SER 129 is not terminus, removing H atom from 'C' /G LEU 110 is not terminus, removing H atom from 'C' 4 messages similar to the above omitted 0 hydrogens added No template found for residue A343 (ASN) Doing nothing > open2 D:/Research/SARS- > CoV-2/2-43/model_building/rbd_2-43/rbd_2-43_three_noh.pdb Summary of feedback from opening <_io.textiowrapper name=""D:/Research/SARS- CoV-2/2-43/model_building/rbd_2-43/rbd_2-43_three_noh.pdb"" mode=""rt"" encoding=""utf-8""> --- warnings | Ignored bad PDB record found on line 4122 END Start residue of secondary structure not found: HELIX 1 1 PHE A 338 ASN A 343 1 6 Start residue of secondary structure not found: HELIX 2 2 TYR A 365 TYR A 369 1 5 Start residue of secondary structure not found: HELIX 3 3 PRO A 384 ASP A 389 1 6 Start residue of secondary structure not found: HELIX 4 4 GLU A 406 GLN A 409 1 4 Start residue of secondary structure not found: HELIX 5 5 LYS A 417 TYR A 421 1 5 31 messages similar to the above omitted Cannot find LINK/SSBOND residue NAG (532 ) Cannot find LINK/SSBOND residue NAG (532 ) Cannot find LINK/SSBOND residue NAG (533 ) Cannot find LINK/SSBOND residue BMA (534 ) Cannot find LINK/SSBOND residue MAN (535 ) Chain information for rbd_2-43_three_noh.pdb #1 --- Chain | Description B | No description available F | No description available G | No description available Chain information for rbd_2-43_three_noh.pdb --- Chain | Description 1.2/B | No description available 1.2/F | No description available 1.2/G | No description available > select H 9437 atoms, 1 model selected > delete atoms sel > delete bonds sel > addh Summary of feedback from adding hydrogens to multiple structures --- warnings | Not adding hydrogens to rbd_2-43_three.pdb #2.2/A TYR 369 CB because it is missing heavy-atom bond partners Not adding hydrogens to rbd_2-43_three.pdb #2.2/A SER 371 CB because it is missing heavy-atom bond partners Not adding hydrogens to rbd_2-43_three.pdb #2.2/A ARG 403 CB because it is missing heavy-atom bond partners Not adding hydrogens to rbd_2-43_three.pdb #2.2/A GLU 406 CB because it is missing heavy-atom bond partners Not adding hydrogens to rbd_2-43_three.pdb #2.2/A ARG 408 CB because it is missing heavy-atom bond partners 103 messages similar to the above omitted notes | No usable SEQRES records for rbd_2-43_three.pdb (#2.2) chain A; guessing termini instead No usable SEQRES records for rbd_2-43_three.pdb (#2.2) chain B; guessing termini instead No usable SEQRES records for rbd_2-43_three.pdb (#2.2) chain C; guessing termini instead No usable SEQRES records for rbd_2-43_three.pdb (#2.2) chain F; guessing termini instead No usable SEQRES records for rbd_2-43_three.pdb (#2.2) chain G; guessing termini instead 4 messages similar to the above omitted Chain-initial residues that are actual N termini: rbd_2-43_three.pdb #2.2/A PHE 329, rbd_2-43_three.pdb #2.2/B PHE 329, rbd_2-43_three.pdb #2.2/C PHE 329, rbd_2-43_three.pdb #2.2/F GLN 1, rbd_2-43_three.pdb #2.2/G GLN 1, rbd_2-43_three.pdb #2.2/H GLN 1, rbd_2-43_three.pdb #2.2/J GLN 1, rbd_2-43_three.pdb #2.2/K GLN 1, rbd_2-43_three.pdb #2.2/L GLN 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: rbd_2-43_three.pdb #2.2/A THR 531, rbd_2-43_three.pdb #2.2/B THR 531, rbd_2-43_three.pdb #2.2/C THR 531, rbd_2-43_three.pdb #2.2/F SER 129, rbd_2-43_three.pdb #2.2/G LEU 110, rbd_2-43_three.pdb #2.2/H SER 129, rbd_2-43_three.pdb #2.2/J SER 129, rbd_2-43_three.pdb #2.2/K LEU 110, rbd_2-43_three.pdb #2.2/L LEU 110 1125 hydrogen bonds rbd_2-43_three.pdb #2.2/A THR 531 is not terminus, removing H atom from 'C' rbd_2-43_three.pdb #2.2/B THR 531 is not terminus, removing H atom from 'C' rbd_2-43_three.pdb #2.2/C THR 531 is not terminus, removing H atom from 'C' rbd_2-43_three.pdb #2.2/F SER 129 is not terminus, removing H atom from 'C' rbd_2-43_three.pdb #2.2/G LEU 110 is not terminus, removing H atom from 'C' 4 messages similar to the above omitted No usable SEQRES records for rbd_2-43_three_noh.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for rbd_2-43_three_noh.pdb (#1.2) chain F; guessing termini instead No usable SEQRES records for rbd_2-43_three_noh.pdb (#1.2) chain G; guessing termini instead Chain-initial residues that are actual N termini: rbd_2-43_three_noh.pdb #1.2/B PHE 329, rbd_2-43_three_noh.pdb #1.2/F GLN 1, rbd_2-43_three_noh.pdb #1.2/G GLN 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: rbd_2-43_three_noh.pdb #1.2/B THR 531, rbd_2-43_three_noh.pdb #1.2/F SER 129, rbd_2-43_three_noh.pdb #1.2/G LEU 110 371 hydrogen bonds rbd_2-43_three_noh.pdb #1.2/B THR 531 is not terminus, removing H atom from 'C' rbd_2-43_three_noh.pdb #1.2/F SER 129 is not terminus, removing H atom from 'C' rbd_2-43_three_noh.pdb #1.2/G LEU 110 is not terminus, removing H atom from 'C' 12584 hydrogens added > select #1 6521 atoms, 6612 bonds, 8 models selected > hide #!2 models > hide #!2.1 models > hide #!2.2 models > hide #2.3 models > select #1.2 6521 atoms, 6612 bonds, 5 models selected > select #1.2 6521 atoms, 6612 bonds, 5 models selected > hide #!1 models > show #!1 models > hide #1.1 models > hide #!1.2 models > hide #1.3 models > show #1.3 models > show #!1.2 models > show #1.1 models > select #1.1 1 model selected > select #1.2 6521 atoms, 6612 bonds, 5 models selected > select #1.3 1 model selected > select #1.2 6521 atoms, 6612 bonds, 5 models selected > select #1.1 1 model selected > close #2 Deleting atomic symmetry model... > open2 D:/Research/SARS- > CoV-2/2-43/n20jun29a_maps/spike_2-43_consensus_sharp.mrc Opened spike_2-43_consensus_sharp.mrc, grid size 384,384,384, pixel 1.06, shown at level 0.068, step 2, values float32 > select #1 6521 atoms, 6612 bonds, 12 models selected > show sel cartoons > close #1 Deleting atomic symmetry model... > open D:\Research\SARS- > CoV-2\2-43\model_building\rbd_2-43\rbd_2-43_three_noh.pdb format PDB Summary of feedback from opening D:\Research\SARS- CoV-2\2-43\model_building\rbd_2-43\rbd_2-43_three_noh.pdb --- warnings | Ignored bad PDB record found on line 4122 END Start residue of secondary structure not found: HELIX 1 1 PHE A 338 ASN A 343 1 6 Start residue of secondary structure not found: HELIX 2 2 TYR A 365 TYR A 369 1 5 Start residue of secondary structure not found: HELIX 3 3 PRO A 384 ASP A 389 1 6 Start residue of secondary structure not found: HELIX 4 4 GLU A 406 GLN A 409 1 4 Start residue of secondary structure not found: HELIX 5 5 LYS A 417 TYR A 421 1 5 31 messages similar to the above omitted Cannot find LINK/SSBOND residue NAG (532 ) Cannot find LINK/SSBOND residue NAG (532 ) Cannot find LINK/SSBOND residue NAG (533 ) Cannot find LINK/SSBOND residue BMA (534 ) Cannot find LINK/SSBOND residue MAN (535 ) Chain information for rbd_2-43_three_noh.pdb #1 --- Chain | Description B | No description available F | No description available G | No description available Chain information for rbd_2-43_three_noh.pdb --- Chain | Description 1.2/B | No description available 1.2/F | No description available 1.2/G | No description available > open2 D:/Research/SARS- > CoV-2/2-43/n20jun29a_maps/spike_2-43_consensus_sharp.mrc Opened spike_2-43_consensus_sharp.mrc, grid size 384,384,384, pixel 1.06, shown at level 0.068, step 2, values float32 > select #1 3374 atoms, 3465 bonds, 12 models selected > select H Nothing selected > delete atoms Deleting atomic symmetry model... Deleting atomic symmetry model... > delete bonds > close #1 Deleting atomic symmetry model... > open D:\Research\SARS- > CoV-2\2-43\model_building\rbd_2-43\rbd_2-43_three_noh.pdb format PDB Summary of feedback from opening D:\Research\SARS- CoV-2\2-43\model_building\rbd_2-43\rbd_2-43_three_noh.pdb --- warnings | Ignored bad PDB record found on line 4122 END Start residue of secondary structure not found: HELIX 1 1 PHE A 338 ASN A 343 1 6 Start residue of secondary structure not found: HELIX 2 2 TYR A 365 TYR A 369 1 5 Start residue of secondary structure not found: HELIX 3 3 PRO A 384 ASP A 389 1 6 Start residue of secondary structure not found: HELIX 4 4 GLU A 406 GLN A 409 1 4 Start residue of secondary structure not found: HELIX 5 5 LYS A 417 TYR A 421 1 5 31 messages similar to the above omitted Cannot find LINK/SSBOND residue NAG (532 ) Cannot find LINK/SSBOND residue NAG (532 ) Cannot find LINK/SSBOND residue NAG (533 ) Cannot find LINK/SSBOND residue BMA (534 ) Cannot find LINK/SSBOND residue MAN (535 ) Chain information for rbd_2-43_three_noh.pdb #1 --- Chain | Description B | No description available F | No description available G | No description available Chain information for rbd_2-43_three_noh.pdb --- Chain | Description 1.2/B | No description available 1.2/F | No description available 1.2/G | No description available > open2 D:/Research/SARS- > CoV-2/2-43/n20jun29a_maps/spike_2-43_consensus_sharp.mrc Opened spike_2-43_consensus_sharp.mrc, grid size 384,384,384, pixel 1.06, shown at level 0.068, step 2, values float32 > addh Summary of feedback from adding hydrogens to rbd_2-43_three_noh.pdb #1.2 --- warnings | Not adding hydrogens to /B TYR 369 CB because it is missing heavy- atom bond partners Not adding hydrogens to /B SER 371 CB because it is missing heavy-atom bond partners Not adding hydrogens to /B ARG 403 CB because it is missing heavy-atom bond partners Not adding hydrogens to /B GLU 406 CB because it is missing heavy-atom bond partners Not adding hydrogens to /B ARG 408 CB because it is missing heavy-atom bond partners 22 messages similar to the above omitted notes | No usable SEQRES records for rbd_2-43_three_noh.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for rbd_2-43_three_noh.pdb (#1.2) chain F; guessing termini instead No usable SEQRES records for rbd_2-43_three_noh.pdb (#1.2) chain G; guessing termini instead Chain-initial residues that are actual N termini: /B PHE 329, /F GLN 1, /G GLN 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /B THR 531, /F SER 129, /G LEU 110 371 hydrogen bonds /B THR 531 is not terminus, removing H atom from 'C' /F SER 129 is not terminus, removing H atom from 'C' /G LEU 110 is not terminus, removing H atom from 'C' 3147 hydrogens added > select #1 6521 atoms, 6612 bonds, 12 models selected No template found for residue G532 (NAG) Doing nothing > select H 3147 atoms, 1 model selected > delete atoms sel > delete bonds sel > close #1.3#1#1.1-2 Deleting atomic symmetry model... > open D:\Research\SARS- > CoV-2\2-43\model_building\rbd_2-43\rbd_2-43_three_noh.pdb format PDB Summary of feedback from opening D:\Research\SARS- CoV-2\2-43\model_building\rbd_2-43\rbd_2-43_three_noh.pdb --- warnings | Ignored bad PDB record found on line 4122 END Start residue of secondary structure not found: HELIX 1 1 PHE A 338 ASN A 343 1 6 Start residue of secondary structure not found: HELIX 2 2 TYR A 365 TYR A 369 1 5 Start residue of secondary structure not found: HELIX 3 3 PRO A 384 ASP A 389 1 6 Start residue of secondary structure not found: HELIX 4 4 GLU A 406 GLN A 409 1 4 Start residue of secondary structure not found: HELIX 5 5 LYS A 417 TYR A 421 1 5 31 messages similar to the above omitted Cannot find LINK/SSBOND residue NAG (532 ) Cannot find LINK/SSBOND residue NAG (532 ) Cannot find LINK/SSBOND residue NAG (533 ) Cannot find LINK/SSBOND residue BMA (534 ) Cannot find LINK/SSBOND residue MAN (535 ) Chain information for rbd_2-43_three_noh.pdb #1 --- Chain | Description B | No description available F | No description available G | No description available Chain information for rbd_2-43_three_noh.pdb --- Chain | Description 1.2/B | No description available 1.2/F | No description available 1.2/G | No description available > open2 D:/Research/SARS-CoV-2/2-43/model_building/rbd_2-43/rbd_2-43_three.pdb Summary of feedback from opening <_io.textiowrapper name=""D:/Research/SARS- CoV-2/2-43/model_building/rbd_2-43/rbd_2-43_three.pdb"" mode=""rt"" encoding=""utf-8""> --- warning | Ignored bad PDB record found on line 23455 END Chain information for rbd_2-43_three.pdb #2 --- Chain | Description A B C | No description available F H J | No description available G K L | No description available > preset cartoons/nucleotides ribbons/slabs Changed 19203 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > hide #!1 models > show #!1 models > hide #!1 models > hide #1.1 models > hide #!1.2 models > hide #1.3 models > hide #2 models > show #2 models > select clear > select clear > style #2 stick Changed 19386 atom styles > close #1.1,3#1#1.2 Deleting atomic symmetry model... Chain information for rbd_2-43_three.pdb --- Chain | Description 1.2/A 1.2/B 1.2/C | No description available 1.2/F 1.2/H 1.2/J | No description available 1.2/G 1.2/K 1.2/L | No description available Deleting atomic symmetry model... > close #1.1,3#1#1.2 Deleting atomic symmetry model... > open2 D:/Research/SARS-CoV-2/2-43/model_building/rbd_2-43/rbd_2-43_three- > coot-0.cif Summary of feedback from opening D:/Research/SARS- CoV-2/2-43/model_building/rbd_2-43/rbd_2-43_three-coot-0.cif --- warnings | Unknown polymer entity '1' near line 68 Unable to fetch template for '---': might be missing bonds Unable to fetch template for '---': might be missing bonds Unable to fetch template for '---': might be missing bonds Unable to fetch template for '---': might be missing bonds Unable to fetch template for '---': might be missing bonds 203 messages similar to the above omitted Skipping struct_conn category: Missing column 'ptnr1_label_asym_id' near line 32 Atom H1 is not in the residue template for PHE #329 in chain A Atom H1 is not in the residue template for GLN #1 in chain L Atom H1 is not in the residue template for GLN #1 in chain H Atom H1 is not in the residue template for GLN #1 in chain G Atom . is not in the residue template for LEU #110 in chain G Atom H1 is not in the residue template for GLN #1 in chain F Atom H1 is not in the residue template for PHE #329 in chain B Atom H1 is not in the residue template for PHE #329 in chain C Atom . is not in the residue template for THR #531 in chain C Atom . is not in the residue template for MAN #536 in chain C Atom H1 is not in the residue template for GLN #1 in chain K Atom . is not in the residue template for LEU #110 in chain K Atom H1 is not in the residue template for GLN #1 in chain J Expected gap or connection between THR #531 and NAG #532 in chain C Expected gap or linking atoms for NAG #532 and NAG #533 in chain C Expected gap or linking atoms for NAG #533 and BMA #534 in chain C Expected gap or linking atoms for BMA #534 and MAN #535 in chain C Expected gap or linking atoms for MAN #535 and MAN #536 in chain C Skipping residue with duplicate label_seq_id 2 in chain J Skipping residue with duplicate label_seq_id 5 in chain J Skipping residue with duplicate label_seq_id 7 in chain J Skipping residue with duplicate label_seq_id 9 in chain J Skipping residue with duplicate label_seq_id 11 in chain J 46 messages similar to the above omitted Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. notes | Fetching CCD NAG from http://ligand- expo.rcsb.org/reports/N/NAG/NAG.cif Fetching CCD BMA from http://ligand-expo.rcsb.org/reports/B/BMA/BMA.cif Fetching CCD MAN from http://ligand-expo.rcsb.org/reports/M/MAN/MAN.cif Combining 4 symmetry atoms into LEU /G:110 . Chain information for rbd_2-43_three-coot-0.cif #1 --- Chain | Description C | No description available J | No description available K | No description available The following atoms were found to have physically impossible anisotropic B-factor (ANISOU) entries. These have been removed in favour of their isotropic B-factors. A329: N Chain information for rbd_2-43_three-coot-0.cif --- Chain | Description 1.2/C | No description available 1.2/J | No description available 1.2/K | No description available > close #1.1,3#1#1.2 Deleting atomic symmetry model... > open2 D:/Research/SARS-CoV-2/2-43/model_building/rbd_2-43/rbd_2-43_three.pdb Summary of feedback from opening <_io.textiowrapper name=""D:/Research/SARS- CoV-2/2-43/model_building/rbd_2-43/rbd_2-43_three.pdb"" mode=""rt"" encoding=""utf-8""> --- warning | Ignored bad PDB record found on line 23455 END Chain information for rbd_2-43_three.pdb #1 --- Chain | Description A B C | No description available F H J | No description available G K L | No description available Chain information for rbd_2-43_three.pdb --- Chain | Description 1.2/A 1.2/B 1.2/C | No description available 1.2/F 1.2/H 1.2/J | No description available 1.2/G 1.2/K 1.2/L | No description available > close #1.1,3#1#1.2 Deleting atomic symmetry model... > open2 D:/Research/SARS- > CoV-2/2-43/model_building/rbd_2-43/rbd_2-43_three_noh.pdb Summary of feedback from opening <_io.textiowrapper name=""D:/Research/SARS- CoV-2/2-43/model_building/rbd_2-43/rbd_2-43_three_noh.pdb"" mode=""rt"" encoding=""utf-8""> --- warning | Ignored bad PDB record found on line 12247 END Chain information for rbd_2-43_three_noh.pdb #1 --- Chain | Description A B C | No description available F H J | No description available G K L | No description available Chain information for rbd_2-43_three_noh.pdb --- Chain | Description 1.2/A 1.2/B 1.2/C | No description available 1.2/F 1.2/H 1.2/J | No description available 1.2/G 1.2/K 1.2/L | No description available > close #1.1,3#1#1.2 Deleting atomic symmetry model... > open2 D:/Research/SARS- > CoV-2/2-43/model_building/rbd_2-43/rbd_2-43_three_pymol.pdb Chain information for rbd_2-43_three_pymol.pdb #1 --- Chain | Description A B C | No description available F H J | No description available G K L | No description available Chain information for rbd_2-43_three_pymol.pdb --- Chain | Description 1.2/A 1.2/B 1.2/C | No description available 1.2/F 1.2/H 1.2/J | No description available 1.2/G 1.2/K 1.2/L | No description available > select H 9264 atoms, 1 model selected > delete atoms sel > delete bonds sel > addh Summary of feedback from adding hydrogens to rbd_2-43_three_pymol.pdb #1.2 --- warnings | Not adding hydrogens to /A TYR 369 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A SER 371 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ARG 403 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A GLU 406 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ARG 408 CB because it is missing heavy-atom bond partners 76 messages similar to the above omitted Unknown hybridization for atoms (C1, C6, C2, C3, C5, O5, O6) of residue type MAN; not adding hydrogens to them Unknown hybridization for atom (O5) of residue type BMA; not adding hydrogens to it Unknown hybridization for atom (CG) of residue type LEU; not adding hydrogens to it Unknown hybridization for atom (OG) of residue type SER; not adding hydrogens to it Unknown hybridization for atoms (CE2, OH, CG, CD1, CZ, CD2, CE1) of residue type TYR; not adding hydrogens to them notes | No usable SEQRES records for rbd_2-43_three_pymol.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for rbd_2-43_three_pymol.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for rbd_2-43_three_pymol.pdb (#1.2) chain C; guessing termini instead No usable SEQRES records for rbd_2-43_three_pymol.pdb (#1.2) chain F; guessing termini instead No usable SEQRES records for rbd_2-43_three_pymol.pdb (#1.2) chain G; guessing termini instead 4 messages similar to the above omitted Chain-initial residues that are actual N termini: /A PHE 329, /B PHE 329, /C PHE 329, /F GLN 1, /G GLN 1, /H GLN 1, /J GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A THR 531, /B THR 531, /C THR 531, /F SER 129, /G LEU 110, /H SER 129, /J SER 129, /K LEU 110, /L LEU 110 1095 hydrogen bonds /A THR 531 is not terminus, removing H atom from 'C' /B THR 531 is not terminus, removing H atom from 'C' /C THR 531 is not terminus, removing H atom from 'C' /F SER 129 is not terminus, removing H atom from 'C' /G LEU 110 is not terminus, removing H atom from 'C' 4 messages similar to the above omitted 9295 hydrogens added > hide HC > open2 D:/Research/SARS- > CoV-2/2-43/n20jun29a_maps/spike_2-43_consensus_sharp.mrc Opened spike_2-43_consensus_sharp.mrc, grid size 384,384,384, pixel 1.06, shown at level 0.068, step 2, values float32 > select clear > select clear > select clear > select clear > volume #1.1.1.1 style surface > volume #1.1.1.1 color #00ffff08 > volume #1.1.1.1 color #00ffff50 > select #1 19417 atoms, 19837 bonds, 12 models selected Traceback (most recent call last): File ""C:\Users\Micah\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\isolde.py"", line 2679, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\Micah\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\isolde.py"", line 2699, in start_sim self.params, self.sim_params, excluded_residues = self.ignored_residues) File ""C:\Users\Micah\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 609, in __init__ raise e File ""C:\Users\Micah\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 591, in __init__ isolde.forcefield_mgr) File ""C:\Users\Micah\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1319, in __init__ template_dict = find_residue_templates(sim_construct.all_residues, ff, ligand_db=ligand_db, logger=session.logger) File ""C:\Users\Micah\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 3044, in find_residue_templates tname, prot_res = find_glycan_template_name_and_link(sugar) File ""C:\Users\Micah\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\amberff\glycam.py"", line 124, in find_glycan_template_name_and_link assert len(bonds) == 1 AssertionError AssertionError File ""C:\Users\Micah\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\amberff\glycam.py"", line 124, in find_glycan_template_name_and_link assert len(bonds) == 1 See log for complete Python traceback. Traceback (most recent call last): File ""C:\Users\Micah\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\isolde.py"", line 2679, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\Micah\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\isolde.py"", line 2699, in start_sim self.params, self.sim_params, excluded_residues = self.ignored_residues) File ""C:\Users\Micah\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 609, in __init__ raise e File ""C:\Users\Micah\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 591, in __init__ isolde.forcefield_mgr) File ""C:\Users\Micah\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1319, in __init__ template_dict = find_residue_templates(sim_construct.all_residues, ff, ligand_db=ligand_db, logger=session.logger) File ""C:\Users\Micah\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 3044, in find_residue_templates tname, prot_res = find_glycan_template_name_and_link(sugar) File ""C:\Users\Micah\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\amberff\glycam.py"", line 124, in find_glycan_template_name_and_link assert len(bonds) == 1 AssertionError AssertionError File ""C:\Users\Micah\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\amberff\glycam.py"", line 124, in find_glycan_template_name_and_link assert len(bonds) == 1 See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 432.00 OpenGL renderer: GeForce RTX 2070 SUPER/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: System manufacturer Model: System Product Name OS: Microsoft Windows 10 Education (Build 19041) Memory: 34,267,029,504 MaxProcessMemory: 137,438,953,344 CPU: 16 AMD Ryzen 7 3700X 8-Core Processor "" }}} " defect closed normal Third Party not a bug all ChimeraX