Opened 5 years ago

Closed 3 years ago

#3377 closed defect (fixed)

Template mismatch errors

Reported by: kartik.manne@… 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:        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/CH235
> structures/CH235p12/ApplyNCS_8/CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb"

Summary of feedback from opening <_io.textiowrapper
name="/home/kartikmanne/Documents/CH235
structures/CH235p12/ApplyNCS_8/CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb"
mode="rt" encoding="utf-8">  
---  
warnings | Ignored bad PDB record found on line 2129  
  
  
Ignored bad PDB record found on line 4538  
  
  
Ignored bad PDB record found on line 5327  
  
  
Ignored bad PDB record found on line 5884  
  
  
Ignored bad PDB record found on line 7428  
  
  
4 messages similar to the above omitted  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2121 messages similar to the above omitted  
Ignored bad PDB record found on line 19397  
  
  
Duplicate atom serial number found: 2127  
Duplicate atom serial number found: 2128  
Duplicate atom serial number found: 2129  
Duplicate atom serial number found: 2130  
Duplicate atom serial number found: 2131  
2402 messages similar to the above omitted  
Ignored bad PDB record found on line 21806  
  
  
Duplicate atom serial number found: 4534  
Duplicate atom serial number found: 4535  
Duplicate atom serial number found: 4536  
Duplicate atom serial number found: 4537  
Duplicate atom serial number found: 4538  
782 messages similar to the above omitted  
Ignored bad PDB record found on line 22595  
  
  
Duplicate atom serial number found: 5321  
Duplicate atom serial number found: 5322  
Duplicate atom serial number found: 5323  
Duplicate atom serial number found: 5324  
Duplicate atom serial number found: 5325  
550 messages similar to the above omitted  
Ignored bad PDB record found on line 23152  
  
  
Duplicate atom serial number found: 5876  
Duplicate atom serial number found: 5877  
Duplicate atom serial number found: 5878  
Duplicate atom serial number found: 5879  
Duplicate atom serial number found: 5880  
1537 messages similar to the above omitted  
Ignored bad PDB record found on line 24696  
  
  
Duplicate atom serial number found: 7418  
Duplicate atom serial number found: 7419  
Duplicate atom serial number found: 7420  
Duplicate atom serial number found: 7421  
Duplicate atom serial number found: 7422  
2088 messages similar to the above omitted  
Ignored bad PDB record found on line 27857  
  
  
Duplicate atom serial number found: 9511  
Duplicate atom serial number found: 9512  
Duplicate atom serial number found: 9513  
Duplicate atom serial number found: 9514  
Duplicate atom serial number found: 9515  
1216 messages similar to the above omitted  
Ignored bad PDB record found on line 29691  
  
  
Duplicate atom serial number found: 10732  
Duplicate atom serial number found: 10733  
Duplicate atom serial number found: 10734  
Duplicate atom serial number found: 10735  
Duplicate atom serial number found: 10736  
1420 messages similar to the above omitted  
Ignored bad PDB record found on line 31843  
  
  
Duplicate atom serial number found: 12157  
Duplicate atom serial number found: 12158  
Duplicate atom serial number found: 12159  
Duplicate atom serial number found: 12160  
Duplicate atom serial number found: 12161  
1792 messages similar to the above omitted  
Ignored bad PDB record found on line 34537  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2121 messages similar to the above omitted  
Ignored bad PDB record found on line 36665  
  
  
Duplicate atom serial number found: 2127  
Duplicate atom serial number found: 2128  
Duplicate atom serial number found: 2129  
Duplicate atom serial number found: 2130  
Duplicate atom serial number found: 2131  
2402 messages similar to the above omitted  
Ignored bad PDB record found on line 39074  
  
  
Duplicate atom serial number found: 4534  
Duplicate atom serial number found: 4535  
Duplicate atom serial number found: 4536  
Duplicate atom serial number found: 4537  
Duplicate atom serial number found: 4538  
782 messages similar to the above omitted  
Ignored bad PDB record found on line 39863  
  
  
Duplicate atom serial number found: 5321  
Duplicate atom serial number found: 5322  
Duplicate atom serial number found: 5323  
Duplicate atom serial number found: 5324  
Duplicate atom serial number found: 5325  
550 messages similar to the above omitted  
Ignored bad PDB record found on line 40420  
  
  
Duplicate atom serial number found: 5876  
Duplicate atom serial number found: 5877  
Duplicate atom serial number found: 5878  
Duplicate atom serial number found: 5879  
Duplicate atom serial number found: 5880  
1537 messages similar to the above omitted  
Ignored bad PDB record found on line 41964  
  
  
Duplicate atom serial number found: 7418  
Duplicate atom serial number found: 7419  
Duplicate atom serial number found: 7420  
Duplicate atom serial number found: 7421  
Duplicate atom serial number found: 7422  
2088 messages similar to the above omitted  
Ignored bad PDB record found on line 45125  
  
  
Duplicate atom serial number found: 9511  
Duplicate atom serial number found: 9512  
Duplicate atom serial number found: 9513  
Duplicate atom serial number found: 9514  
Duplicate atom serial number found: 9515  
1216 messages similar to the above omitted  
Ignored bad PDB record found on line 46959  
  
  
Duplicate atom serial number found: 10732  
Duplicate atom serial number found: 10733  
Duplicate atom serial number found: 10734  
Duplicate atom serial number found: 10735  
Duplicate atom serial number found: 10736  
1420 messages similar to the above omitted  
Ignored bad PDB record found on line 49111  
  
  
Duplicate atom serial number found: 12157  
Duplicate atom serial number found: 12158  
Duplicate atom serial number found: 12159  
Duplicate atom serial number found: 12160  
Duplicate atom serial number found: 12161  
1792 messages similar to the above omitted  
Ignored bad PDB record found on line 51805  
  
  
Ignored bad PDB record found on line 51806  
  
Chain information for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb #1  
---  
Chain | Description  
A B G | No description available  
A B G | No description available  
C E H | No description available  
D F I | No description available  
  

> set bgColor white

> addh

Summary of feedback from adding hydrogens to
CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb #1  
---  
notes | No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb
(#1) chain A; guessing termini instead  
No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb (#1)
chain A; guessing termini instead  
No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb (#1)
chain B; guessing termini instead  
No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb (#1)
chain B; guessing termini instead  
No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb (#1)
chain C; guessing termini instead  
7 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A GLU 32, /A NAG 518, /B
GLU 32, /B NAG 518, /C GLN 1, /D GLU 1, /E GLN 1, /F GLU 1, /G GLU 32, /G NAG
518, /H GLN 1, /I GLU 1  
Chain-initial residues that are not actual N termini: /A CYS 157, /A GLY 312,
/A PHE 361, /A ASN 409, /B CYS 157, /B GLY 312, /B PHE 361, /B ASN 409, /C GLY
134, /D TRP 96, /E GLY 134, /F TRP 96, /G CYS 157, /G GLY 312, /G PHE 361, /G
ASN 409, /H GLY 134, /I TRP 96  
Chain-final residues that are actual C termini: /A NAG 540, /B NAG 540, /G NAG
540  
Chain-final residues that are not actual C termini: /A VAL 503, /A ASN 147, /A
ILE 309, /A THR 359, /A ASN 398, /B VAL 503, /B ASN 147, /B ILE 309, /B THR
359, /B ASN 398, /C CYS 216, /C SER 128, /D GLY 212, /D TRP 94, /E CYS 216, /E
SER 128, /F GLY 212, /F TRP 94, /G VAL 503, /G ASN 147, /G ILE 309, /G THR
359, /G ASN 398, /H CYS 216, /H SER 128, /I GLY 212, /I TRP 94  
2328 hydrogen bonds  
/A VAL 503 is not terminus, removing H atom from 'C'  
/A ASN 147 is not terminus, removing H atom from 'C'  
/A ILE 309 is not terminus, removing H atom from 'C'  
/A THR 359 is not terminus, removing H atom from 'C'  
/A ASN 398 is not terminus, removing H atom from 'C'  
22 messages similar to the above omitted  
984 hydrogens added  
  

> select #1

42843 atoms, 43326 bonds, 33 pseudobonds, 2 models selected  

> addh

Summary of feedback from adding hydrogens to
CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb #1  
---  
notes | No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb
(#1) chain A; guessing termini instead  
No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb (#1)
chain A; guessing termini instead  
No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb (#1)
chain B; guessing termini instead  
No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb (#1)
chain B; guessing termini instead  
No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb (#1)
chain C; guessing termini instead  
7 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A GLU 32, /A NAG 518, /B
GLU 32, /B NAG 518, /C GLN 1, /D GLU 1, /E GLN 1, /F GLU 1, /G GLU 32, /G NAG
518, /H GLN 1, /I GLU 1  
Chain-initial residues that are not actual N termini: /A CYS 157, /A GLY 312,
/A PHE 361, /A ASN 409, /B CYS 157, /B GLY 312, /B PHE 361, /B ASN 409, /C GLY
134, /D TRP 96, /E GLY 134, /F TRP 96, /G CYS 157, /G GLY 312, /G PHE 361, /G
ASN 409, /H GLY 134, /I TRP 96  
Chain-final residues that are actual C termini: /A NAG 540, /B NAG 540, /G NAG
540  
Chain-final residues that are not actual C termini: /A VAL 503, /A ASN 147, /A
ILE 309, /A THR 359, /A ASN 398, /B VAL 503, /B ASN 147, /B ILE 309, /B THR
359, /B ASN 398, /C CYS 216, /C SER 128, /D GLY 212, /D TRP 94, /E CYS 216, /E
SER 128, /F GLY 212, /F TRP 94, /G VAL 503, /G ASN 147, /G ILE 309, /G THR
359, /G ASN 398, /H CYS 216, /H SER 128, /I GLY 212, /I TRP 94  
2286 hydrogen bonds  
/A VAL 503 is not terminus, removing H atom from 'C'  
/A ASN 147 is not terminus, removing H atom from 'C'  
/A ILE 309 is not terminus, removing H atom from 'C'  
/A THR 359 is not terminus, removing H atom from 'C'  
/A ASN 398 is not terminus, removing H atom from 'C'  
22 messages similar to the above omitted  
0 hydrogens added  
  

> open2 "/home/kartikmanne/Documents/CH235
> structures/CH235p12/cryosparc_P9_J22_009_volume_map_sharp_local.mrc"

Opened cryosparc_P9_J22_009_volume_map_sharp_local.mrc, grid size 320,320,320,
pixel 1.08, shown at level 0.772, step 2, values float32  

> isolde restrain ligands #1

> clipper associate #2 toModel #1

Chain information for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/G | No description available  
1.2/A 1.2/B 1.2/G | No description available  
1.2/C 1.2/E 1.2/H | No description available  
1.2/D 1.2/F 1.2/I | No description available  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

QWidget::repaint: Recursive repaint detected  

> select #1

42843 atoms, 43326 bonds, 33 pseudobonds, 15 models selected  

No template found for residue A517 (NAG)  

Adding hydrogens  
Summary of feedback from adding hydrogens to
CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb #1.2  
---  
notes | No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb
(#1.2) chain A; guessing termini instead  
No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb (#1.2)
chain A; guessing termini instead  
No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb (#1.2)
chain B; guessing termini instead  
No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb (#1.2)
chain B; guessing termini instead  
No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8.pdb (#1.2)
chain C; guessing termini instead  
7 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A GLU 32, /A NAG 518, /B
GLU 32, /B NAG 518, /C GLN 1, /D GLU 1, /E GLN 1, /F GLU 1, /G GLU 32, /G NAG
518, /H GLN 1, /I GLU 1  
Chain-initial residues that are not actual N termini: /A CYS 157, /A GLY 312,
/A PHE 361, /A ASN 409, /B CYS 157, /B GLY 312, /B PHE 361, /B ASN 409, /C GLY
134, /D TRP 96, /E GLY 134, /F TRP 96, /G CYS 157, /G GLY 312, /G PHE 361, /G
ASN 409, /H GLY 134, /I TRP 96  
Chain-final residues that are actual C termini: /A NAG 540, /B NAG 540, /G NAG
540  
Chain-final residues that are not actual C termini: /A VAL 503, /A ASN 147, /A
ILE 309, /A THR 359, /A ASN 398, /B VAL 503, /B ASN 147, /B ILE 309, /B THR
359, /B ASN 398, /C CYS 216, /C SER 128, /D GLY 212, /D TRP 94, /E CYS 216, /E
SER 128, /F GLY 212, /F TRP 94, /G VAL 503, /G ASN 147, /G ILE 309, /G THR
359, /G ASN 398, /H CYS 216, /H SER 128, /I GLY 212, /I TRP 94  
2286 hydrogen bonds  
/A VAL 503 is not terminus, removing H atom from 'C'  
/A ASN 147 is not terminus, removing H atom from 'C'  
/A ILE 309 is not terminus, removing H atom from 'C'  
/A THR 359 is not terminus, removing H atom from 'C'  
/A ASN 398 is not terminus, removing H atom from 'C'  
22 messages similar to the above omitted  
0 hydrogens added  
  

No template found for residue A517 (NAG)  

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 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 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/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2791, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__  
raise e  
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 1117, in createSystem  
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
ignoreExternalBonds=ignoreExternalBonds)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 893, in
_getResidueTemplateMatches  
raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
(res.index+1, res.name, ', '.join(match[0].name for match in allMatches)))  
Exception: Multiple matching templates found for residue 452 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
Exception: Multiple matching templates found for residue 452 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 893, in
_getResidueTemplateMatches  
raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
(res.index+1, res.name, ', '.join(match[0].name for match in allMatches)))  
  
See log for complete Python traceback.  
  

> close session

Deleting atomic symmetry model...  

> open2 "/home/kartikmanne/Documents/CH235
> structures/CH235p12/ApplyNCS_8/CH235p12-M5-G458Y-GnT1-_apply_ncs_8-2.pdb"

Summary of feedback from opening <_io.textiowrapper
name="/home/kartikmanne/Documents/CH235
structures/CH235p12/ApplyNCS_8/CH235p12-M5-G458Y-GnT1-_apply_ncs_8-2.pdb"
mode="rt" encoding="utf-8">  
---  
warnings | Ignored bad PDB record found on line 2129  
  
  
Ignored bad PDB record found on line 4538  
  
  
Ignored bad PDB record found on line 5327  
  
  
Ignored bad PDB record found on line 5884  
  
  
Ignored bad PDB record found on line 7428  
  
  
4 messages similar to the above omitted  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2121 messages similar to the above omitted  
Ignored bad PDB record found on line 16100  
  
  
Duplicate atom serial number found: 2127  
Duplicate atom serial number found: 2128  
Duplicate atom serial number found: 2129  
Duplicate atom serial number found: 2130  
Duplicate atom serial number found: 2131  
2402 messages similar to the above omitted  
Ignored bad PDB record found on line 18509  
  
  
Duplicate atom serial number found: 4534  
Duplicate atom serial number found: 4535  
Duplicate atom serial number found: 4536  
Duplicate atom serial number found: 4537  
Duplicate atom serial number found: 4538  
782 messages similar to the above omitted  
Ignored bad PDB record found on line 19298  
  
  
Duplicate atom serial number found: 5321  
Duplicate atom serial number found: 5322  
Duplicate atom serial number found: 5323  
Duplicate atom serial number found: 5324  
Duplicate atom serial number found: 5325  
550 messages similar to the above omitted  
Ignored bad PDB record found on line 19855  
  
  
Duplicate atom serial number found: 5876  
Duplicate atom serial number found: 5877  
Duplicate atom serial number found: 5878  
Duplicate atom serial number found: 5879  
Duplicate atom serial number found: 5880  
1537 messages similar to the above omitted  
Ignored bad PDB record found on line 21399  
  
  
Duplicate atom serial number found: 7418  
Duplicate atom serial number found: 7419  
Duplicate atom serial number found: 7420  
Duplicate atom serial number found: 7421  
Duplicate atom serial number found: 7422  
2088 messages similar to the above omitted  
Ignored bad PDB record found on line 23494  
  
  
Duplicate atom serial number found: 9511  
Duplicate atom serial number found: 9512  
Duplicate atom serial number found: 9513  
Duplicate atom serial number found: 9514  
Duplicate atom serial number found: 9515  
1216 messages similar to the above omitted  
Ignored bad PDB record found on line 24717  
  
  
Duplicate atom serial number found: 10732  
Duplicate atom serial number found: 10733  
Duplicate atom serial number found: 10734  
Duplicate atom serial number found: 10735  
Duplicate atom serial number found: 10736  
1420 messages similar to the above omitted  
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Duplicate atom serial number found: 12157  
Duplicate atom serial number found: 12158  
Duplicate atom serial number found: 12159  
Duplicate atom serial number found: 12160  
Duplicate atom serial number found: 12161  
1792 messages similar to the above omitted  
Ignored bad PDB record found on line 27943  
  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2121 messages similar to the above omitted  
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Duplicate atom serial number found: 2127  
Duplicate atom serial number found: 2128  
Duplicate atom serial number found: 2129  
Duplicate atom serial number found: 2130  
Duplicate atom serial number found: 2131  
2402 messages similar to the above omitted  
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Duplicate atom serial number found: 4534  
Duplicate atom serial number found: 4535  
Duplicate atom serial number found: 4536  
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Duplicate atom serial number found: 4538  
782 messages similar to the above omitted  
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Duplicate atom serial number found: 5321  
Duplicate atom serial number found: 5322  
Duplicate atom serial number found: 5323  
Duplicate atom serial number found: 5324  
Duplicate atom serial number found: 5325  
550 messages similar to the above omitted  
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Duplicate atom serial number found: 5876  
Duplicate atom serial number found: 5877  
Duplicate atom serial number found: 5878  
Duplicate atom serial number found: 5879  
Duplicate atom serial number found: 5880  
1537 messages similar to the above omitted  
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Duplicate atom serial number found: 7418  
Duplicate atom serial number found: 7419  
Duplicate atom serial number found: 7420  
Duplicate atom serial number found: 7421  
Duplicate atom serial number found: 7422  
2088 messages similar to the above omitted  
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Duplicate atom serial number found: 9511  
Duplicate atom serial number found: 9512  
Duplicate atom serial number found: 9513  
Duplicate atom serial number found: 9514  
Duplicate atom serial number found: 9515  
1216 messages similar to the above omitted  
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Duplicate atom serial number found: 10732  
Duplicate atom serial number found: 10733  
Duplicate atom serial number found: 10734  
Duplicate atom serial number found: 10735  
Duplicate atom serial number found: 10736  
1420 messages similar to the above omitted  
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Duplicate atom serial number found: 12157  
Duplicate atom serial number found: 12158  
Duplicate atom serial number found: 12159  
Duplicate atom serial number found: 12160  
Duplicate atom serial number found: 12161  
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Chain information for CH235p12-M5-G458Y-GnT1-_apply_ncs_8-2.pdb #1  
---  
Chain | Description  
A B G | No description available  
A B G | No description available  
C E H | No description available  
D F I | No description available  
  
Chain information for CH235p12-M5-G458Y-GnT1-_apply_ncs_8-2.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/G | No description available  
1.2/A 1.2/B 1.2/G | No description available  
1.2/C 1.2/E 1.2/H | No description available  
1.2/D 1.2/F 1.2/I | No description available  
  

> open2 "/home/kartikmanne/Documents/CH235
> structures/CH235p12/cryosparc_P9_J22_009_volume_map_sharp_local.mrc"

Opened cryosparc_P9_J22_009_volume_map_sharp_local.mrc, grid size 320,320,320,
pixel 1.08, shown at level 0.772, step 2, values float32  

> addh

Summary of feedback from adding hydrogens to
CH235p12-M5-G458Y-GnT1-_apply_ncs_8-2.pdb #1.2  
---  
notes | No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8-2.pdb
(#1.2) chain A; guessing termini instead  
No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8-2.pdb (#1.2)
chain A; guessing termini instead  
No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8-2.pdb (#1.2)
chain B; guessing termini instead  
No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8-2.pdb (#1.2)
chain B; guessing termini instead  
No usable SEQRES records for CH235p12-M5-G458Y-GnT1-_apply_ncs_8-2.pdb (#1.2)
chain C; guessing termini instead  
7 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A GLU 32, /A NAG 518, /B
GLU 32, /B NAG 518, /C GLN 1, /D GLU 1, /E GLN 1, /F GLU 1, /G GLU 32, /G NAG
518, /H GLN 1, /I GLU 1  
Chain-initial residues that are not actual N termini: /A CYS 157, /A GLY 312,
/A PHE 361, /A ASN 409, /B CYS 157, /B GLY 312, /B PHE 361, /B ASN 409, /C GLY
134, /D TRP 96, /E GLY 134, /F TRP 96, /G CYS 157, /G GLY 312, /G PHE 361, /G
ASN 409, /H GLY 134, /I TRP 96  
Chain-final residues that are actual C termini: /A NAG 540, /B NAG 540, /G NAG
540  
Chain-final residues that are not actual C termini: /A VAL 503, /A ASN 147, /A
ILE 309, /A THR 359, /A ASN 398, /B VAL 503, /B ASN 147, /B ILE 309, /B THR
359, /B ASN 398, /C CYS 216, /C SER 128, /D GLY 212, /D TRP 94, /E CYS 216, /E
SER 128, /F GLY 212, /F TRP 94, /G VAL 503, /G ASN 147, /G ILE 309, /G THR
359, /G ASN 398, /H CYS 216, /H SER 128, /I GLY 212, /I TRP 94  
2328 hydrogen bonds  
/A VAL 503 is not terminus, removing H atom from 'C'  
/A ASN 147 is not terminus, removing H atom from 'C'  
/A ILE 309 is not terminus, removing H atom from 'C'  
/A THR 359 is not terminus, removing H atom from 'C'  
/A ASN 398 is not terminus, removing H atom from 'C'  
22 messages similar to the above omitted  
984 hydrogens added  
  

> isolde restrain ligands #1

> clipper associate #2 toModel #1

> select #1

42843 atoms, 43326 bonds, 33 pseudobonds, 15 models selected  

No template found for residue A517 (NAG)  

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 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/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2799, in _handle_bad_template  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__  
raise e  
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 1117, in createSystem  
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
ignoreExternalBonds=ignoreExternalBonds)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 893, in
_getResidueTemplateMatches  
raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
(res.index+1, res.name, ', '.join(match[0].name for match in allMatches)))  
Exception: Multiple matching templates found for residue 452 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
Exception: Multiple matching templates found for residue 452 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 893, in
_getResidueTemplateMatches  
raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
(res.index+1, res.name, ', '.join(match[0].name for match in allMatches)))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/kartikmanne/.local/share/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 "/home/kartikmanne/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__  
raise e  
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 1117, in createSystem  
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom,
ignoreExternalBonds=ignoreExternalBonds)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 893, in
_getResidueTemplateMatches  
raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
(res.index+1, res.name, ', '.join(match[0].name for match in allMatches)))  
Exception: Multiple matching templates found for residue 452 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
Exception: Multiple matching templates found for residue 452 (NAG):
GLYCAM_0VA, GLYCAM_0VB, GLYCAM_0WA, GLYCAM_0WB, GLYCAM_0YA, GLYCAM_0YB,
GLYCAM_0vA, GLYCAM_0vB, GLYCAM_0wA, GLYCAM_0wB, GLYCAM_0yA, GLYCAM_0yB.  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 893, in
_getResidueTemplateMatches  
raise Exception('Multiple matching templates found for residue %d (%s): %s.' %
(res.index+1, res.name, ', '.join(match[0].name for match in allMatches)))  
  
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 (3)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Template mismatch errors

comment:2 by Tristan Croll, 5 years ago

As it happens, I'm just working on improving the handling of unrecognised/incorrect residues at the moment! The most common cause of this sort of issue is that the geometry of the glycosidic bonds is bad, causing addh to incorrectly add hydrogens (try "addh template true" to see if that helps). If you're able to share the coordinates (directly to me at tic20@…), I'll be happy to take a look to work out what's going on. I'll be sure to keep them confidential.

comment:3 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed

Closing out old tickets - ISOLDE's had functionality to help with issues like this for some time now.

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