Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#3308 closed defect (duplicate)

User-supplied template does not match the residue

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

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
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
> /home/kartikmanne/Documents/VRC40/cryosparc_P4_J12_008_volume_map_sharp_local-
> zflip.mrc

Opened cryosparc_P4_J12_008_volume_map_sharp_local-zflip.mrc, grid size
320,320,320, pixel 1.08, shown at level 0.667, step 2, values float32  

> close session

> open2
> /home/kartikmanne/Documents/VRC40/VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif

Summary of feedback from opening
/home/kartikmanne/Documents/VRC40/VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 1674  
Unable to infer polymer connectivity due to unspecified label_seq_id for
residue "NAG" near line 1720  
Missing entity information. Treating each chain as a separate entity.  
Missing second residue in struct_conn "C00002"  
Missing first residue in struct_conn "C00020"  
Missing first residue in struct_conn "C00021"  
Missing first residue in struct_conn "C00022"  
Missing first residue in struct_conn "C00023"  
Missing first residue in struct_conn "C00024"  
57 messages similar to the above omitted  
Missing second residue in struct_conn "C00082"  
Missing second residue in struct_conn "C00083"  
Missing first residue in struct_conn "C00084"  
Missing first residue in struct_conn "C00085"  
Missing first residue in struct_conn "C00086"  
Missing first residue in struct_conn "C00087"  
Missing first residue in struct_conn "C00088"  
5 messages similar to the above omitted  
Missing second residue in struct_conn "C00094"  
Missing second residue in struct_conn "C00095"  
Missing first residue in struct_conn "C00096"  
Missing first residue in struct_conn "C00097"  
Missing first residue in struct_conn "C00098"  
Missing first residue in struct_conn "C00099"  
Missing first residue in struct_conn "C00100"  
13 messages similar to the above omitted  
Missing second residue in struct_conn "C00114"  
Missing second residue in struct_conn "C00115"  
Missing first residue in struct_conn "C00116"  
Missing first residue in struct_conn "C00117"  
Missing first residue in struct_conn "C00118"  
Missing first residue in struct_conn "C00119"  
Missing first residue in struct_conn "C00120"  
69 messages similar to the above omitted  
Missing second residue in struct_conn "C00228"  
Missing second residue in struct_conn "C00229"  
Missing first residue in struct_conn "C00230"  
Missing first residue in struct_conn "C00231"  
Missing first residue in struct_conn "C00232"  
Missing first residue in struct_conn "C00233"  
Missing first residue in struct_conn "C00234"  
8 messages similar to the above omitted  
Missing second residue in struct_conn "C00301"  
Missing first residue in struct_conn "C00319"  
Missing first residue in struct_conn "C00320"  
Missing first residue in struct_conn "C00321"  
Missing first residue in struct_conn "C00322"  
Missing first residue in struct_conn "C00323"  
57 messages similar to the above omitted  
Missing second residue in struct_conn "C00381"  
Missing second residue in struct_conn "C00382"  
Missing first residue in struct_conn "C00383"  
Missing first residue in struct_conn "C00384"  
Missing first residue in struct_conn "C00385"  
Missing first residue in struct_conn "C00386"  
Missing first residue in struct_conn "C00387"  
5 messages similar to the above omitted  
Missing second residue in struct_conn "C00393"  
Missing second residue in struct_conn "C00394"  
Missing first residue in struct_conn "C00395"  
Missing first residue in struct_conn "C00396"  
Missing first residue in struct_conn "C00397"  
Missing first residue in struct_conn "C00398"  
Missing first residue in struct_conn "C00399"  
13 messages similar to the above omitted  
Missing second residue in struct_conn "C00413"  
Missing second residue in struct_conn "C00414"  
Missing first residue in struct_conn "C00415"  
Missing first residue in struct_conn "C00416"  
Missing first residue in struct_conn "C00417"  
Missing first residue in struct_conn "C00418"  
Missing first residue in struct_conn "C00419"  
69 messages similar to the above omitted  
Missing second residue in struct_conn "C00527"  
Missing second residue in struct_conn "C00528"  
Missing first residue in struct_conn "C00529"  
Missing first residue in struct_conn "C00530"  
Missing first residue in struct_conn "C00531"  
Missing first residue in struct_conn "C00532"  
Missing first residue in struct_conn "C00533"  
8 messages similar to the above omitted  
Missing second residue in struct_conn "C00600"  
Missing first residue in struct_conn "C00618"  
Missing first residue in struct_conn "C00619"  
Missing first residue in struct_conn "C00620"  
Missing first residue in struct_conn "C00621"  
Missing first residue in struct_conn "C00622"  
57 messages similar to the above omitted  
Missing second residue in struct_conn "C00680"  
Missing second residue in struct_conn "C00681"  
Missing first residue in struct_conn "C00682"  
Missing first residue in struct_conn "C00683"  
Missing first residue in struct_conn "C00684"  
Missing first residue in struct_conn "C00685"  
Missing first residue in struct_conn "C00686"  
5 messages similar to the above omitted  
Missing second residue in struct_conn "C00692"  
Missing second residue in struct_conn "C00693"  
Missing first residue in struct_conn "C00694"  
Missing first residue in struct_conn "C00695"  
Missing first residue in struct_conn "C00696"  
Missing first residue in struct_conn "C00697"  
Missing first residue in struct_conn "C00698"  
13 messages similar to the above omitted  
Missing second residue in struct_conn "C00712"  
Missing second residue in struct_conn "C00713"  
Missing first residue in struct_conn "C00714"  
Missing first residue in struct_conn "C00715"  
Missing first residue in struct_conn "C00716"  
Missing first residue in struct_conn "C00717"  
Missing first residue in struct_conn "C00718"  
69 messages similar to the above omitted  
Missing second residue in struct_conn "C00826"  
Missing second residue in struct_conn "C00827"  
Missing first residue in struct_conn "C00828"  
Missing first residue in struct_conn "C00829"  
Missing first residue in struct_conn "C00830"  
Missing first residue in struct_conn "C00831"  
Missing first residue in struct_conn "C00832"  
8 messages similar to the above omitted  
Bad residue range for struct_conf "1" near line 110  
Bad residue range for struct_conf "2" near line 111  
Bad residue range for struct_conf "3" near line 112  
Bad residue range for struct_conf "4" near line 113  
Bad residue range for struct_conf "5" near line 114  
22 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "D 3" near line 1383  
Invalid sheet range for struct_sheet_range "I 3" near line 1402  
Invalid sheet range for struct_sheet_range "N 3" near line 1421  
Invalid sheet range for struct_sheet_range "A 2" near line 1425  
Invalid sheet range for struct_sheet_range "B 2" near line 1427  
4 messages similar to the above omitted  
Atom H1 is not in the residue template for ALA #32 in chain A  
Atom H1 is not in the residue template for ALA #512 in chain B  
Atom H1 is not in the residue template for GLN #1 in chain C  
Atom H1 is not in the residue template for GLN #1 in chain D  
Atom H1 is not in the residue template for ALA #32 in chain E  
7 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' near line 50550  
Skipping chem_comp category: Missing column 'type' near line 50714  
Skipping chem_comp category: Missing column 'type' near line 50878  
  
Chain information for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif #1  
---  
Chain | Description  
A E I | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> open2
> /home/kartikmanne/Documents/VRC40/cryosparc_P4_J12_008_volume_map_sharp_local-
> zflip.mrc

Opened cryosparc_P4_J12_008_volume_map_sharp_local-zflip.mrc, grid size
320,320,320, pixel 1.08, shown at level 0.667, step 2, values float32  

> set bgColor white

> addh

Summary of feedback from adding hydrogens to
VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif #1  
---  
notes | No usable SEQRES records for
VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif (#1) chain A; guessing
termini instead  
No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
(#1) chain B; guessing termini instead  
No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
(#1) chain C; guessing termini instead  
No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
(#1) chain D; guessing termini instead  
No usable SEQRES records for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif
(#1) chain E; guessing termini instead  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A ALA 32, /B ALA 512, /C
GLN 1, /D GLN 1, /E ALA 32, /I ALA 32  
Chain-initial residues that are not actual N termini: /A HIS 67, /A LYS 190,
/A ASP 412, /C ALA 129, /C ALA 151, /C THR 175, /C TYR 209, /C ALA 129, /C ALA
151, /C THR 175, /C TYR 209, /C ALA 129, /C ALA 151, /C THR 175, /C TYR 209,
/E HIS 67, /E LYS 190, /E ASP 412, /I HIS 67, /I LYS 190, /I ASP 412  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A VAL 505, /A ALA 59, /A
GLN 184, /A ILE 396, /B ASP 664, /C SER 230, /C SER 127, /C SER 143, /C GLY
172, /C THR 198, /C SER 127, /C SER 143, /C GLY 172, /C THR 198, /C SER 127,
/C SER 143, /C GLY 172, /C THR 198, /D CYS 214, /E VAL 505, /E ALA 59, /E GLN
184, /E ILE 396, /I VAL 505, /I ALA 59, /I GLN 184, /I ILE 396  
2461 hydrogen bonds  
/A VAL 505 is not terminus, removing H atom from 'C'  
/A ALA 59 is not terminus, removing H atom from 'C'  
/A GLN 184 is not terminus, removing H atom from 'C'  
/A ILE 396 is not terminus, removing H atom from 'C'  
/B ASP 664 is not terminus, removing H atom from 'C'  
22 messages similar to the above omitted  
1530 hydrogens added  
  

> clipper associate #2 toModel #1

Chain information for VRC40_apply_ncs_60-1-RSR70_real_space_refined.cif  
---  
Chain | Description  
1.2/A 1.2/E 1.2/I | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> select #1

50160 atoms, 50724 bonds, 321 pseudobonds, 13 models selected  

QWidget::repaint: Recursive repaint detected  

No template found for residue A506 (NAG)  

Excluding residue  

No template found for residue A508 (NAG)  

Excluding residue  

No template found for residue A509 (NAG)  

Excluding residue  

No template found for residue A512 (NAG)  

Excluding residue  

No template found for residue A515 (NAG)  

Excluding residue  

No template found for residue A517 (NAG)  

Excluding residue  

No template found for residue A519 (BMA)  

Excluding residue  

No template found for residue A521 (MAN)  

Excluding residue  

No template found for residue A522 (NAG)  

Excluding residue  

No template found for residue A527 (MAN)  

Excluding residue  

No template found for residue A528 (MAN)  

Excluding residue  

No template found for residue A529 (NAG)  

Excluding residue  

No template found for residue A531 (NAG)  

Excluding residue  

No template found for residue A534 (NAG)  

Excluding residue  

No template found for residue A537 (NAG)  

Excluding residue  

No template found for residue A540 (NAG)  

Excluding residue  

No template found for residue A543 (NAG)  

Excluding residue  

No template found for residue A544 (NAG)  

Excluding residue  

No template found for residue B598 (CYS)  

Excluding residue  

No template found for residue B598 (CYS)  

Excluding residue  

No template found for residue B598 (CYS)  

Excluding residue  

No template found for residue B604 (CYS)  

Excluding residue  

No template found for residue B604 (CYS)  

Excluding residue  

No template found for residue B604 (CYS)  

Excluding residue  

No template found for residue B605 (CYS)  

Excluding residue  

No template found for residue B605 (CYS)  

Excluding residue  

No template found for residue B605 (CYS)  

Excluding residue  

No template found for residue C22 (CYS)  

Excluding residue  

No template found for residue C22 (CYS)  

Excluding residue  

No template found for residue C22 (CYS)  

Excluding residue  

No template found for residue C101 (CYS)  

Excluding residue  

No template found for residue C101 (CYS)  

Excluding residue  

No template found for residue C101 (CYS)  

Excluding residue  

No template found for residue C155 (CYS)  

Excluding residue  

No template found for residue C155 (CYS)  

Excluding residue  

No template found for residue C155 (CYS)  

Excluding residue  

No template found for residue C211 (CYS)  

Excluding residue  

No template found for residue C211 (CYS)  

Excluding residue  

No template found for residue C211 (CYS)  

Excluding residue  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_4YB does not match the residue 440
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0YB does not match the residue 441
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_4YB does not match the residue 441
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_4YB does not match the residue 443
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_4YB does not match the residue 445
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_4YB does not match the residue 446
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_3MB does not match the residue 447
(BMA)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0MA does not match the residue 448
(MAN)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_4YB does not match the residue 448
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0MA does not match the residue 452
(MAN)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_0MA does not match the residue 452
(MAN)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_4YB does not match the residue 452
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template GLYCAM_4YB does not match the residue 453
(NAG)  
  
During handling of the above exception, another exception occurred:  
  
[nuked center of log for length]

File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 275, in
_model_changed_cb  
self.update_scatter()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 372, in update_scatter  
if not self.visible:  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 283, in visible  
return self.parent.isVisible()  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QVBoxLayout has been deleted  
  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/ramaplot.py", line 279, in parent  
return self.container.parentWidget()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 430.40
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: TYAN
Model: B7105F48TV8HR-2T-G
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 64 Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz
Cache Size: 22528 KB
Graphics:
	04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)
	Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]
	Kernel driver in use: ast

Change History (5)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Third Party
Description: modified (diff)
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → User-supplied template does not match the residue

comment:2 by Eric Pettersen, 5 years ago

Resolution: → duplicate
Status: assigned → closed

in reply to:  3 ; comment:3 by Tristan Croll, 5 years ago 

I meant to add a comment to this via the wiki, but it seems to have been 
eaten... anyway, perhaps it would be a good idea to have another quiet 
word with the Phenix team about their mmCIF writer? Might be taken more 
seriously coming from Greg than from me - he appears to know the format 
inside and out now.

On 2020-05-26 18:18, ChimeraX wrote:

comment:4 by Eric Pettersen, 5 years ago

Just FYI, Greg isn't cc'ed on this ticket...

in reply to:  5 ; comment:5 by Tristan Croll, 5 years ago 

Will bring it up in the Thursday meeting.

On 2020-05-26 18:32, ChimeraX wrote:
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