Opened 4 years ago

Closed 4 years ago

#5630 closed defect (fixed)

ISOLDE: various errors

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  

> 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 #1, grid size
384,384,384, pixel 0.65, shown at level 0.118, step 2, values float32  

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

Chain information for 6c6b_ref34_2_2.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> lighting soft

> set bgColor white

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for 6c6b_ref34_2_2.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B | No description available  
2.2/C | No description available  
2.2/D | No description available  
  
Done loading forcefield  

> clipper associate #2 toModel #1

Invalid "toModel" argument: Must specify 1 structure, got 0 for "#1"  

> clipper associate #1 toModel #2.2

Opened cryosparc_P3_J819_004_volume_map_sharp.mrc as #2.1.1.1, grid size
384,384,384, pixel 0.65, shown at step 1, values float32  

Falling back to using screens root_visual.  

> isolde start

> addh

Summary of feedback from adding hydrogens to 6c6b_ref34_2_2.pdb #2.2  
---  
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 (#2.2) chain A;
guessing termini instead  
No usable SEQRES records for 6c6b_ref34_2_2.pdb (#2.2) chain B; guessing
termini instead  
No usable SEQRES records for 6c6b_ref34_2_2.pdb (#2.2) chain C; guessing
termini instead  
No usable SEQRES records for 6c6b_ref34_2_2.pdb (#2.2) 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  
  

> hide HC

> select #2.2

27042 atoms, 27609 bonds, 1 pseudobond, 1505 residues, 6 models selected  

> isolde sim start sel

ISOLDE: stopped sim  

> ui mousemode right select

> select clear

> select #2.2/A,B

25233 atoms, 25659 bonds, 1 pseudobond, 1447 residues, 2 models selected  

> select #2.2/A,C

3769 atoms, 4069 bonds, 119 residues, 1 model selected  

> select #2.2/A,B,D

26141 atoms, 26638 bonds, 1 pseudobond, 1476 residues, 2 models selected  

> select clear

> select #2.2/A,B,D

26141 atoms, 26638 bonds, 1 pseudobond, 1476 residues, 2 models selected  

> select #2.2/A,C,D

4677 atoms, 5048 bonds, 148 residues, 1 model selected  
ISOLDE: stopped sim  

> select #2.2/C,D

1809 atoms, 1950 bonds, 58 residues, 1 model selected  
ISOLDE: stopped sim  

> isolde adjust distances #2.2/A,C,D kappa 50

ISOLDE: stopped sim  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/validation/unparameterised.py", line 185, in
_fix_selected_unparameterised_residue  
fix_residue_to_match_md_template(self.session, r, template,
cif_template=ccd_template)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/atomic/template_utils.py", line 329, in
fix_residue_to_match_md_template  
fix_residue_from_template(residue, cif_template, template_indices=ccd_indices)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/atomic/template_utils.py", line 203, in
fix_residue_from_template  
matched_nodes, residue_extra, template_extra =
find_maximal_isomorphous_fragment(residue, template,
limit_template_indices=template_indices, match_by=match_by)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/atomic/template_utils.py", line 156, in
find_maximal_isomorphous_fragment  
rg = residue_graph(residue, label=match_by)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/atomic/template_utils.py", line 102, in residue_graph  
return make_graph_from_residue(residue, label=label)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/graph/__init__.py", line
26, in make_graph_from_residue  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/graph/__init__.py", line
26, in make_graph_from_residue  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/validation/unparameterised.py", line 185, in
_fix_selected_unparameterised_residue  
fix_residue_to_match_md_template(self.session, r, template,
cif_template=ccd_template)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/atomic/template_utils.py", line 329, in
fix_residue_to_match_md_template  
fix_residue_from_template(residue, cif_template, template_indices=ccd_indices)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/atomic/template_utils.py", line 203, in
fix_residue_from_template  
matched_nodes, residue_extra, template_extra =
find_maximal_isomorphous_fragment(residue, template,
limit_template_indices=template_indices, match_by=match_by)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/atomic/template_utils.py", line 156, in
find_maximal_isomorphous_fragment  
rg = residue_graph(residue, label=match_by)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/atomic/template_utils.py", line 102, in residue_graph  
return make_graph_from_residue(residue, label=label)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/graph/__init__.py", line
26, in make_graph_from_residue  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/graph/__init__.py", line
26, in make_graph_from_residue  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
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: OP1, HO3'  
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  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/validation/unparameterised.py", line 185, in
_fix_selected_unparameterised_residue  
fix_residue_to_match_md_template(self.session, r, template,
cif_template=ccd_template)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/atomic/template_utils.py", line 329, in
fix_residue_to_match_md_template  
fix_residue_from_template(residue, cif_template, template_indices=ccd_indices)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/atomic/template_utils.py", line 203, in
fix_residue_from_template  
matched_nodes, residue_extra, template_extra =
find_maximal_isomorphous_fragment(residue, template,
limit_template_indices=template_indices, match_by=match_by)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/atomic/template_utils.py", line 156, in
find_maximal_isomorphous_fragment  
rg = residue_graph(residue, label=match_by)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/atomic/template_utils.py", line 102, in residue_graph  
return make_graph_from_residue(residue, label=label)  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/graph/__init__.py", line
26, in make_graph_from_residue  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/graph/__init__.py", line
26, in make_graph_from_residue  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  
Fetching CCD GNG from http://ligand-expo.rcsb.org/reports/G/GNG/GNG.cif  
Fetching CCD GMP from http://ligand-expo.rcsb.org/reports/G/GMP/GMP.cif  
Deleted the following atoms from residue C C16: OP1  
Deleted the following atoms from residue C D-10: OP1  
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 C D-7: OP1  
Deleted the following atoms from residue C C13: OP1  
Deleted the following atoms from residue G C11: OP1  
Deleted the following atoms from residue G C8: OP1  

> select del

Expected an objects specifier or a keyword  

> select #2.2/A:9

1 atom, 1 residue, 1 model selected  

> delete sel

> select #2.2/A,C,D

4726 atoms, 5097 bonds, 147 residues, 1 model selected  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2726, in
_start_sim_or_toggle_pause  
self.start_sim()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2780, in
start_sim  
sm.start_sim()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim  
sh.start_sim()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim  
self._prepare_sim()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/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.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2726, in
_start_sim_or_toggle_pause  
self.start_sim()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2780, in
start_sim  
sm.start_sim()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim  
sh.start_sim()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim  
self._prepare_sim()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/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.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2726, in
_start_sim_or_toggle_pause  
self.start_sim()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py", line 2780, in
start_sim  
sm.start_sim()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim  
sh.start_sim()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim  
self._prepare_sim()  
File "/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF-
ChimeraX/lib/python3.8/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        7.0G         51G        158M        3.9G         54G
	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 (2)

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: various errors

comment:2 by Tristan Croll, 4 years ago

Resolution: → fixed
Status: assigned → closed

First error (RuntimeError: edges should be a n x 2 array of unsigned ints!) should be fixed in the coming release. The second one looks like the user's CUDA installation is messed up and missing a library. Not really much I can do about that since it's an anonymous report.

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