Opened 5 years ago

Closed 5 years ago

#3500 closed defect (not a bug)

Problem simulating glycans

Reported by: mar2294@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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             "

Change History (5)

comment:1 by Tristan Croll, 5 years ago

Platform: → all
Project: → ChimeraX

Hmm... any chance you can send me a copy of the model (off-list, at tic20@…) so I can take a look? The root cause is clear enough (and the next version of ISOLDE will give you a much more informative message): one of your sugars is linked to another residue twice (which as far as I'm aware isn't biologically possible - it isn't supported by the GLYCAM forcefield, in any case). In the meantime I can help get you up and running easily enough.

One other issue that it looks like you tripped over early on: simulations currently fail to start if you have a glycan linked to an N-terminal asparagine. I'll be looking into that.

comment:2 by Eric Pettersen, 5 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Status: new → assigned
Summary: ChimeraX bug report submission → Problem simulating glycans

comment:3 by Eric Pettersen, 5 years ago

Reported by Micah Rapp

in reply to:  4 ; comment:4 by mar2294@…, 5 years ago 

Hi Tristian,

I think I've figured it out. Glycans came a little close with some residues
so when I wrote the connect records (to maintain some disulfides ChimeraX
was breaking), it linked them together.

The glycans weren't supposed to be linked to a terminal asparagine, but
looks like a bond somehow accidentally got broken so it was reading as one.

Thanks for the quick response and helping me track the problem down.

Best,
Micah Rapp

On Mon, Jul 13, 2020 at 6:41 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:5 by Greg Couch, 5 years ago

Resolution: → not a bug
Status: assigned → closed

Micah figured it out.

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