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#14467 assigned defect

Residue NAG is linked to a glycan, but no parameters are available for this type of linkage

Reported by:	cnp@…	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-5.15.0-91-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /u/au591166/Desktop/B0AT1/Refinement/B0AT1_sharpened_map.ccp4 format
> ccp4

Opened B0AT1_sharpened_map.ccp4 as #1, grid size 300,300,300, pixel 1.04,
shown at level 2.91, step 2, values float32  

> open /u/au591166/Desktop/B0AT1/Refinement/RealSpaceRefine_7/RSR7_Leu_CHS-
> coot-9.pdb

Chain information for RSR7_Leu_CHS-coot-9.pdb #2  
---  
Chain | Description  
C | No description available  
D | No description available  
  

> volume #1 step 1

> volume #1 level 5.793

> isolde start

> set selectionWidth 4

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 30 residues in model #2 to IUPAC-IUB
standards.  
Chain information for RSR7_Leu_CHS-coot-9.pdb  
---  
Chain | Description  
2.2/C | No description available  
2.2/D | No description available  
  

> clipper associate #1 toModel #2

Opened B0AT1_sharpened_map.ccp4 as #2.1.1.1, grid size 300,300,300, pixel
1.04, shown at step 1, values float32  

> ui mousemode right select

Drag select of 627 atoms, 725 residues, 633 bonds, 2 pseudobonds  

> clipper isolate /C:5-609,621,628,630-632/D maskRadius 4.0 focus false

Drag select of 7499 atoms, 725 residues, 7703 bonds, 2 pseudobonds  

> clipper isolate /C:5-610,615-618,621-635/D maskRadius 4.0 focus false

> volume #2.1.1.1 level 2.605

Drag select of 7550 atoms, 725 residues, 7757 bonds, 2 pseudobonds  

> clipper isolate /C-D maskRadius 4.0 focus false

> clipper isolate /C-D maskRadius 5.0 focus false

> isolde sim start /C-D

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde parameterise sel override false

Running ANTECHAMBER command: /usr/lib/ucsf-
chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmprwhjacw5/ante.in.mol2 -fi mol2 -o /tmp/tmprwhjacw5/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2 -dr n  
(CHS) ``  
(CHS) `Welcome to antechamber 20.0: molecular input file processor.`  
(CHS) ``  
(CHS) `Info: Finished reading file (/tmp/tmprwhjacw5/ante.in.mol2); atoms read
(84), bonds read (87).`  
(CHS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(CHS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(CHS) ``  
(CHS) ``  
(CHS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(CHS) `Info: Total number of electrons: 268; net charge: -1`  
(CHS) ``  
(CHS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`  
(CHS) ``  
(CHS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-
chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1`  
(CHS) ``  
(CHS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(CHS) ``  
Charges for residue CHS determined  
OpenMM ffXML file CHS written to the current working directory.  
New template added to forcefield as USER_CHS. This ligand should now work in
all remaining simulations for this session. To use in future sessions, load
the ffXML file with ISOLDE's Load Residue MD Definition(s) button.  

> view #2.2:LEU

> view #2.2:601

> view #2.2:6010

No objects specified.  

> view #2.2:610

> view #2.2:605

> view #2.2:620

> view #2.2:leu

> volume #2.1.1.1 level 12.25

> view #2.2/C:8

> view #2.2/C:48

> clipper spotlight

> isolde sim start /C:622

ISOLDE: started sim  

> volume #2.1.1.1 level 5.072

> ui mousemode right "isolde tug selection"

[Repeated 1 time(s)]

> ui mousemode right "isolde tug residue"

[Repeated 1 time(s)]

> ui mousemode right "isolde tug atom"

[Repeated 1 time(s)]

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> ui mousemode right select

Drag select of 449 atoms, 725 residues, 456 bonds, 2 pseudobonds  

> clipper isolate /C:5-609,629,633/D maskRadius 5.0 focus false

Drag select of 7793 atoms, 725 residues, 7997 bonds, 2 pseudobonds  

> clipper isolate /C:5-610,615-618,621-635/D maskRadius 5.0 focus false

Drag select of 7844 atoms, 725 residues, 8051 bonds, 2 pseudobonds  

> clipper isolate /C-D maskRadius 5.0 focus false

> isolde sim start /C-D

ISOLDE: started sim  

> ui tool show "Ramachandran Plot"

> isolde pepflip /C:282

[Repeated 1 time(s)]Unable to flip peptide bond after 50 rounds. Giving up.  

> view #2.2/C:48

> volume #2.1.1.1 level 14.2

> view #2.2/C:621

> undo

> view #2.2/C:621

> isolde sim pause

> open /u/au591166/Desktop/B0AT1/Refinement/RealSpaceRefine_7/RSR7_Leu_CHS-
> coot-9.pdb

Chain information for RSR7_Leu_CHS-coot-9.pdb #1  
---  
Chain | Description  
C | No description available  
D | No description available  
  

> hide #!1 models

> isolde sim resume

> show #!1 models

> hide #!1 models

> show #!1 models

> isolde sim pause

> hide #!1 models

> ui mousemode right distance

> distance #2.2/C:621@H #2.2/C:277@O

Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C LEU 621 H and PHE 277 O:
1.844Å  

> distance #2.2/C:280@OG #2.2/C:621@H

Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C SER 280 OG and LEU 621 H:
2.976Å  

> distance #2.2/C:278@O #2.2/C:621@H

Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C SER 278 O and LEU 621 H:
3.754Å  

> ~distance #2.2/C:280@OG #2.2/C:621@H

> distance #2.2/C:49@O #2.2/C:280@OG

Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C CYS 49 O and SER 280 OG:
4.403Å  

> undo

> select add #2.2

12923 atoms, 13130 bonds, 5 pseudobonds, 748 residues, 16 models selected  

> select add #2.2

12923 atoms, 13130 bonds, 5 pseudobonds, 748 residues, 16 models selected  

> hide #!2.2 models

> show #!2.2 models

> select add #2.2

12923 atoms, 13130 bonds, 5 pseudobonds, 748 residues, 16 models selected  

> select add #2.2

12923 atoms, 13130 bonds, 5 pseudobonds, 748 residues, 16 models selected  

> select add #2.2

12923 atoms, 13130 bonds, 5 pseudobonds, 748 residues, 16 models selected  

> ui mousemode right select

> select clear

> close #3

> ui mousemode right distance

> hide #!1 models

> distance #2.2/C:49@O #2.2/C:621@H

Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C CYS 49 O and LEU 621 H: 3.909Å  

> distance #2.2/C:280@OG #2.2/C:621@H

Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C SER 280 OG and LEU 621 H:
2.976Å  

> distance #2.2/C:277@O #2.2/C:621@H

Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C PHE 277 O and LEU 621 H:
1.844Å  

> distance #2.2/C:278@O #2.2/C:621@H

Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C SER 278 O and LEU 621 H:
3.754Å  

> distance #2.2/C:48@O #2.2/C:621@H

Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C PHE 48 O and LEU 621 H: 4.396Å  

> hide #3.1 models

> show #!1 models

> hide #!2.2 models

> show #!2.2 models

> distance #2.2/C:48@O #1/C:621@N

Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C PHE 48 O and RSR7_Leu_CHS-
coot-9.pdb #1/C LEU 621 N: 2.814Å  

> ~distance #2.2/C:48@O #1/C:621@N

> distance #2.2/C:49@O #1/C:621@N

Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C CYS 49 O and RSR7_Leu_CHS-
coot-9.pdb #1/C LEU 621 N: 2.970Å  

> show #3.1 models

> ~distance #2.2/C:48@O #2.2/C:621@H

> distance #1/C:621@N #2.2/C:48@O

Distance between RSR7_Leu_CHS-coot-9.pdb #1/C LEU 621 N and RSR7_Leu_CHS-
coot-9.pdb #2.2/C PHE 48 O: 2.814Å  

> distance #2.2/C:280@OG #1/C:621@N

Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C SER 280 OG and RSR7_Leu_CHS-
coot-9.pdb #1/C LEU 621 N: 2.291Å  

> distance #2.2/C:278@O #1/C:621@N

Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C SER 278 O and RSR7_Leu_CHS-
coot-9.pdb #1/C LEU 621 N: 3.867Å  

> hide #!3 models

> hide #3.1 models

> ui mousemode right distance

> distance #1/C:129@HH #2.2/C:621@O

Distance between RSR7_Leu_CHS-coot-9.pdb #1/C TYR 129 HH and RSR7_Leu_CHS-
coot-9.pdb #2.2/C LEU 621 O: 2.553Å  

> show #!3 models

> show #3.1 models

> distance #2.2/C:53@H #2.2/C:621@O

Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C GLY 53 H and LEU 621 O: 1.916Å  

> distance #2.2/C:129@HH #2.2/C:621@O

Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C TYR 129 HH and LEU 621 O:
1.814Å  

> hide #!3 models

> hide #!1 models

> isolde sim resume

> view #2.2/C:622

> volume #2.1.1.1 level 11.47

> view #2.2/C:623

> volume #2.1.1.1 level 10.03

> view #2.2/C:624

> view #2.2/C:625

> volume #2.1.1.1 level 8.594

> isolde sim pause

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 9 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save /u/au591166/Desktop/B0AT1/Refinement/RealSpaceRefine_7/RSR7_Leu_CHS-
> coot-9_ISOLDE.pdb models #2

> close #3#2.3#2.1-2

Deleting atomic symmetry model...  

> close #1

Deleting atomic symmetry model...  

> hide #2 models

> show #2 models

> hide #2 models

> close

Deleting atomic symmetry model...  

> open /u/au591166/Desktop/B0AT1/Refinement/B0AT1_sharpened_map.ccp4 format
> ccp4

Opened B0AT1_sharpened_map.ccp4 as #1, grid size 300,300,300, pixel 1.04,
shown at level 2.91, step 2, values float32  

> open /u/au591166/Desktop/B0AT1/Refinement/RealSpaceRefine_11/RSR11_Leu_CHS-
> coot-10.pdb

Chain information for RSR11_Leu_CHS-coot-10.pdb #2  
---  
Chain | Description  
C | No description available  
C | No description available  
D | No description available  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 40 residues in model #2 to IUPAC-IUB
standards.  
Chain information for RSR11_Leu_CHS-coot-10.pdb  
---  
Chain | Description  
2.2/C | No description available  
2.2/C | No description available  
2.2/D | No description available  
  

> clipper associate #1 toModel #2

Opened B0AT1_sharpened_map.ccp4 as #2.1.1.1, grid size 300,300,300, pixel
1.04, shown at step 1, values float32  
Traceback (most recent call last):  
File "/u/au591166/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 84, in
_populate_unparameterised_residue_table  
template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db,
logger=self.session.logger)  
File "/u/au591166/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3014, in
find_residue_templates  
templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res)  
File "/u/au591166/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 269, in
find_glycan_anchor_name  
raise RuntimeError('Residue {} {}{} is linked to a glycan, but no '  
RuntimeError: Residue NAG C620 is linked to a glycan, but no parameters are
available for this type of linkage.  
  
RuntimeError: Residue NAG C620 is linked to a glycan, but no parameters are
available for this type of linkage.  
  
File "/u/au591166/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 269, in
find_glycan_anchor_name  
raise RuntimeError('Residue {} {}{} is linked to a glycan, but no '  
  
See log for complete Python traceback.  
  

> view #2.2/C:620

> ui mousemode right select

Drag select of 546 atoms, 725 residues, 547 bonds, 4 pseudobonds  

> clipper isolate /C:5-609/D maskRadius 5.0 focus false

Drag select of 7499 atoms, 725 residues, 7703 bonds, 4 pseudobonds  

> clipper isolate /C:5-610,615-618,621-635/D maskRadius 5.0 focus false

Drag select of 7550 atoms, 725 residues, 7757 bonds, 4 pseudobonds  

> clipper isolate /C-D maskRadius 5.0 focus false

> volume #2.1.1.1 level 7.732

> clipper isolate /C-D maskRadius 5.0 focus false

> select clear

> volume #2.1.1.1 level 6.292

Drag select of 7550 atoms, 725 residues, 7757 bonds, 4 pseudobonds  

> clipper isolate /C-D maskRadius 5.0 focus false

> volume #2.1.1.1 level 4.051

> select clear

[Repeated 2 time(s)]Drag select of 7550 atoms, 725 residues, 7757 bonds, 4
pseudobonds  

> clipper isolate /C-D maskRadius 5.0 focus false

> volume #2.1.1.1 level 6.452

> volume #2.1.1.1 level 5.491

> select clear

[Repeated 3 time(s)]

> ui mousemode right rotate

> isolde sim start /C:56

ISOLDE: started sim  

> isolde pepflip /C:60

[Repeated 4 time(s)]

> isolde pepflip /C:56

[Repeated 1 time(s)]

> isolde pepflip /C:55

[Repeated 1 time(s)]

> isolde sim pause

> ui tool show "Ramachandran Plot"

> view #2.2/C:634

Traceback (most recent call last):  
File "/u/au591166/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 84, in
_populate_unparameterised_residue_table  
template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db,
logger=self.session.logger)  
File "/u/au591166/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3014, in
find_residue_templates  
templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res)  
File "/u/au591166/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 269, in
find_glycan_anchor_name  
raise RuntimeError('Residue {} {}{} is linked to a glycan, but no '  
RuntimeError: Residue NAG C620 is linked to a glycan, but no parameters are
available for this type of linkage.  
  
RuntimeError: Residue NAG C620 is linked to a glycan, but no parameters are
available for this type of linkage.  
  
File "/u/au591166/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 269, in
find_glycan_anchor_name  
raise RuntimeError('Residue {} {}{} is linked to a glycan, but no '  
  
See log for complete Python traceback.  
  

> ui mousemode right select

> select /C:634@C09

1 atom, 1 residue, 1 model selected  
Drag select of 154 atoms, 154 bonds  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start
> /C:187,472,475,477-481,484-485,558-560,578,582,585-586,589,633-634

Sim termination reason: None  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File "/u/au591166/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 84, in
_populate_unparameterised_residue_table  
template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db,
logger=self.session.logger)  
File "/u/au591166/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3014, in
find_residue_templates  
templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res)  
File "/u/au591166/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 269, in
find_glycan_anchor_name  
raise RuntimeError('Residue {} {}{} is linked to a glycan, but no '  
RuntimeError: Residue NAG C620 is linked to a glycan, but no parameters are
available for this type of linkage.  
  
RuntimeError: Residue NAG C620 is linked to a glycan, but no parameters are
available for this type of linkage.  
  
File "/u/au591166/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 269, in
find_glycan_anchor_name  
raise RuntimeError('Residue {} {}{} is linked to a glycan, but no '  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 545.23.08
OpenGL renderer: NVIDIA RTX A5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xubuntu
XDG_SESSION_DESKTOP=xubuntu
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:1.0
Manufacturer: LENOVO
Model: 30E0003SMT
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD Ryzen Threadripper PRO 3955WX 16-Cores
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       7.7Gi        48Gi       162Mi       6.8Gi        54Gi
	Swap:          975Mi       0.0Ki       975Mi

Graphics:
	61:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102GL [RTX A5000] [10de:2231] (rev a1)	
	Subsystem: Hewlett-Packard Company GA102GL [RTX A5000] [103c:147e]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by pett, 21 months ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Residue NAG is linked to a glycan, but no parameters are available for this type of linkage

Reported by Clara

comment:2 by Tristan Croll, 21 months ago

I should definitely replace this traceback with a more informative (and
better-formatted) error message, but the most likely reason for this is
that the offending NAG is connected to another sugar via an incorrect
linkage (the bond should go from the NAG O3, O4 or O6 to the C1 of the next
sugar). If you check it and you’re sure it’s correct, then you’re dealing
with something particularly unusual that isn’t covered by the GLYCAM force
field. That would be a somewhat difficult scenario to tackle.

On Wed, 24 Jan 2024 at 17:54, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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