Context Navigation

← Previous Ticket
Next Ticket →

#5631 closed defect (fixed)

ISOLDE: fix unparameterized residues: Residue already deleted

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

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.45.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed
'ChimeraX_ISOLDE-1.2.2-cp38-cp38-manylinux_2_17_x86_64.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
/home/Jinek/MPacesa/.cache/ChimeraX/1.2/installers/ChimeraX_ISOLDE-1.2.2-cp38-cp38-manylinux_2_17_x86_64.whl  
Requirement already satisfied: ChimeraX-Core~=1.2.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-ISOLDE==1.2.2) (1.2.5)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-ISOLDE==1.2.2) (1.0)  
Requirement already satisfied: ChimeraX-Clipper~=0.16.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-ISOLDE==1.2.2) (0.16.0)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=3.1.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-ISOLDE==1.2.2) (3.1.3)  
Requirement already satisfied: ChimeraX-Atomic~=1.13.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-ISOLDE==1.2.2) (1.13.2)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.1)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (2.4.1)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (2.3)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.0)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (2.0)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (2.0.1)  
Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-
ConnectStructure~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.4)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.5)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1)  
Requirement already satisfied: ChimeraX-IO~=1.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-
DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.0.1)  
Requirement already satisfied: ChimeraX-UI~=1.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.7.6)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0)  
Requirement already satisfied: ChimeraX-Map~=1.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.2)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.3.1)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.1)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (2.0)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (2.0)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-MapSeries~=2.0->ChimeraX-
Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in
/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0)  
Installing collected packages: ChimeraX-ISOLDE  
Successfully installed ChimeraX-ISOLDE-1.2.2  
  

WARNING: You are using pip version 21.0.1; however, version 21.3.1 is
available.  
You should consider upgrading via the
'/programs/x86_64-linux/chimerax/1.2.5-c7/bin/chimerax -m pip install
--upgrade pip' command.  
  

> open /home/Jinek/MPacesa/Data/6c6b_cryo/WorkingModel/6c6b_ref34_2_2.pdb

Chain information for 6c6b_ref34_2_2.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> open
> /home/Jinek/MPacesa/Data/6c6b_cryo/Maps/cryosparc_P3_J819_004_volume_map_sharp.mrc

Opened cryosparc_P3_J819_004_volume_map_sharp.mrc as #2, grid size
384,384,384, pixel 0.65, shown at level 0.118, step 2, values float32  

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for 6c6b_ref34_2_2.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
  
Done loading forcefield  
Opened cryosparc_P3_J819_004_volume_map_sharp.mrc as #1.1.1.1, grid size
384,384,384, pixel 0.65, shown at step 1, values float32  

> select #2.2/A,C,D

Nothing selected  

> select #1.2/A,C,D

3091 atoms, 3462 bonds, 148 residues, 1 model selected  
ISOLDE: stopped sim  

> addh

Summary of feedback from adding hydrogens to 6c6b_ref34_2_2.pdb #1.2  
---  
warnings | Not adding hydrogens to /A A 9 O3' because it is missing heavy-atom
bond partners  
Not adding hydrogens to /C G 8 C2' because it is missing heavy-atom bond
partners  
Not adding hydrogens to /C A 9 C2' because it is missing heavy-atom bond
partners  
Not adding hydrogens to /C A 10 C2' because it is missing heavy-atom bond
partners  
Not adding hydrogens to /C G 11 C2' because it is missing heavy-atom bond
partners  
13 messages similar to the above omitted  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A A 9 O3'  
notes | No usable SEQRES records for 6c6b_ref34_2_2.pdb (#1.2) chain A;
guessing termini instead  
No usable SEQRES records for 6c6b_ref34_2_2.pdb (#1.2) chain B; guessing
termini instead  
No usable SEQRES records for 6c6b_ref34_2_2.pdb (#1.2) chain C; guessing
termini instead  
No usable SEQRES records for 6c6b_ref34_2_2.pdb (#1.2) chain D; guessing
termini instead  
Chain-initial residues that are actual N termini: /A A 9, /B ASP 2, /C DC -9,
/D DT -18  
Chain-initial residues that are not actual N termini: /B LYS 775  
Chain-final residues that are actual C termini: /A U 98, /C A 19, /D DG 10  
Chain-final residues that are not actual C termini: /B GLY 1366, /B GLU 766  
1231 hydrogen bonds  
Adding 'H' to /B LYS 775  
/B GLY 1366 is not terminus, removing H atom from 'C'  
12862 hydrogens added  
  

> select #1.2/A:9

1 atom, 1 residue, 1 model selected  

> delete sel

Traceback (most recent call last):  
File "/home/Jinek/MPacesa/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 177, in
_fix_selected_unparameterised_residue  
indices = [i for i in range(table.rowCount()) if table.item(i, 0).data[0].name
== residue.name]  
File "/home/Jinek/MPacesa/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 177, in
<listcomp>  
indices = [i for i in range(table.rowCount()) if table.item(i, 0).data[0].name
== residue.name]  
File "atomic_cpp/cymol.pyx", line 1181, in
chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "atomic_cpp/cymol.pyx", line 1181, in
chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/Jinek/MPacesa/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 177, in
_fix_selected_unparameterised_residue  
indices = [i for i in range(table.rowCount()) if table.item(i, 0).data[0].name
== residue.name]  
File "/home/Jinek/MPacesa/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 177, in
<listcomp>  
indices = [i for i in range(table.rowCount()) if table.item(i, 0).data[0].name
== residue.name]  
File "atomic_cpp/cymol.pyx", line 1181, in
chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "atomic_cpp/cymol.pyx", line 1181, in
chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  
Deleted the following atoms from residue G D-12: OP1  
Deleted the following atoms from residue G D-15: OP1  
Deleted the following atoms from residue G C11: OP1  
Deleted the following atoms from residue G C8: OP1  
Deleted the following atoms from residue A D-6: OP1  
Deleted the following atoms from residue A D-11: OP1  
Deleted the following atoms from residue A D-13: OP1  
Deleted the following atoms from residue A D-17: OP1  
Deleted the following atoms from residue A C19: HO3', OP1  
Deleted the following atoms from residue A C17: OP1  
Deleted the following atoms from residue A C15: OP1  
Deleted the following atoms from residue A C10: OP1  
Deleted the following atoms from residue A C9: OP1  
Deleted the following atoms from residue C D-7: OP1  
Deleted the following atoms from residue C D-10: OP1  
Deleted the following atoms from residue C C16: OP1  
Deleted the following atoms from residue C C13: OP1  

> select #1.2/A,C,D

4726 atoms, 5097 bonds, 147 residues, 1 model selected  
Traceback (most recent call last):  
File "/home/Jinek/MPacesa/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2726, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/Jinek/MPacesa/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2780, in start_sim  
sm.start_sim()  
File "/home/Jinek/MPacesa/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim  
sh.start_sim()  
File "/home/Jinek/MPacesa/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim  
self._prepare_sim()  
File "/home/Jinek/MPacesa/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1561, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/simtk/openmm/app/simulation.py", line
105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/simtk/openmm/openmm.py", line 17752, in
__init__  
this = _openmm.new_Context(*args)  
simtk.openmm.OpenMMException: Error compiling program: nvrtc: error: failed to
open libnvrtc-builtins.so.  
Make sure that libnvrtc-builtins.so is installed correctly.  
  
simtk.openmm.OpenMMException: Error compiling program: nvrtc: error: failed to
open libnvrtc-builtins.so.  
Make sure that libnvrtc-builtins.so is installed correctly.  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/simtk/openmm/openmm.py", line 17752, in
__init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 440.82
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 5820 Tower
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 Intel(R) Xeon(R) W-2245 CPU @ 3.90GHz
Cache Size: 16896 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        6.0G         52G        121M        4.3G         55G
	Swap:           31G          0B         31G

Graphics:
	0000:17:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P4000] [10de:1bb1] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11a3]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Change History (5)

comment:1 by Eric Pettersen, 4 years ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → ISOLDE: fix unparameterized residues: Residue already deleted

in reply to: 2 ; follow-up: 2 comment:2 by Tristan Croll, 4 years ago

Hmm... looks like I need to add another `changes` callback.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 18 November 2021 21:16
Cc: chimerax-bug-report@cgl.ucsf.edu <chimerax-bug-report@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #5631: ISOLDE: fix unparameterized residues: Residue already deleted (was: ChimeraX bug report submission)

#5631: ISOLDE: fix unparameterized residues: Residue already deleted
--------------------------------------------+---------------------------
          Reporter:  chimerax-bug-report@…  |      Owner:  Tristan Croll
              Type:  defect                 |     Status:  assigned
          Priority:  normal                 |  Milestone:
         Component:  Third Party            |    Version:
        Resolution:                         |   Keywords:
        Blocked By:                         |   Blocking:
Notify when closed:                         |   Platform:  all
           Project:  ChimeraX               |
--------------------------------------------+---------------------------
Changes (by Eric Pettersen):

 * status:  new => assigned
 * component:  Unassigned => Third Party
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => Tristan Croll


--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5631#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:3 by Eric Pettersen, 4 years ago

Depending on your usage context, you can also directly ask if various atomic class instances (including Residue) are deleted by checking their '.deleted' attribute.

comment:4 by Tristan Croll, 4 years ago

Bugger... meant to fix this for this release, but it slipped my mind. Oh well... will get it on the next. :)

comment:5 by Tristan Croll, 3 years ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed in the new GUI.

Note: See TracTickets for help on using tickets.

Download in other formats: