id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
5746	OpenMMException: Error compiling program: nvrtc: error: failed to open libnvrtc-builtins.so.	venkatareddy@…	Tristan Croll	"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 /nfs/userdocs/sch/walsh/MwergedPDB-KKSP.pdb format pdb

Chain information for MwergedPDB-KKSP.pdb #1  
---  
Chain | Description  
A R | No description available  
B S | No description available  
C T | No description available  
D U | No description available  
E V | No description available  
F W | No description available  
G X | No description available  
H Y | No description available  
I Z | No description available  
J a | No description available  
K b | No description available  
L c | No description available  
M d | No description available  
N e | No description available  
O f | No description available  
P g | No description available  
Q h | No description available  


open /nfs/userdocs/sch/walsh/Downloads/preholo_3A_J319_C2_sharp.mrc format
mrc

Opened preholo_3A_J319_C2_sharp.mrc as #2, grid size 360,360,360, pixel 1.06,
shown at level 0.305, step 2, values float32  

addh

Summary of feedback from adding hydrogens to MwergedPDB-KKSP.pdb #1  
---  
notes | No usable SEQRES records for MwergedPDB-KKSP.pdb (#1) chain A;
guessing termini instead  
No usable SEQRES records for MwergedPDB-KKSP.pdb (#1) chain B; guessing
termini instead  
No usable SEQRES records for MwergedPDB-KKSP.pdb (#1) chain C; guessing
termini instead  
No usable SEQRES records for MwergedPDB-KKSP.pdb (#1) chain D; guessing
termini instead  
No usable SEQRES records for MwergedPDB-KKSP.pdb (#1) chain E; guessing
termini instead  
29 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /B ASP 3, /C TYR 6, /D TYR
4, /E MET 1, /F MET 1, /G THR 2, /H VAL 21, /I ALA 2, /J SER 6, /M PHE 21, /O
MET 1, /P SER 2, /Q PRO 37, /S ASP 3, /T TYR 6, /U TYR 4, /V MET 1, /W MET 1,
/X THR 2, /Y VAL 21, /Z ALA 2, /a SER 6, /d PHE 21, /f MET 1, /g SER 2, /h PRO
37  
Chain-initial residues that are not actual N termini: /A GLY 11, /A GLU 197,
/C VAL 225, /D LEU 52, /D SER 62, /D ALA 209, /E ARG 132, /G LEU 187, /G ASP
211, /H THR 132, /I THR 30, /I SER 231, /J PHE 40, /J GLY 184, /K ASP 2, /K
GLY 24, /K ASP 32, /K VAL 179, /L THR 79, /L ASP 127, /L MET 173, /L ASN 252,
/M LEU 194, /N GLY 14, /O VAL 117, /O PRO 163, /P SER 57, /P ASN 128, /P VAL
164, /P PRO 199, /P ALA 237, /Q LEU 120, /R GLY 11, /R GLU 197, /T VAL 225, /U
LEU 52, /U SER 62, /U ALA 209, /V ARG 132, /X LEU 187, /X ASP 211, /Y THR 132,
/Z THR 30, /Z SER 231, /a PHE 40, /a GLY 184, /b ASP 2, /b GLY 24, /b ASP 32,
/b VAL 179, /c THR 79, /c ASP 127, /c MET 173, /c ASN 252, /d LEU 194, /e GLY
14, /f VAL 117, /f PRO 163, /g SER 57, /g ASN 128, /g VAL 164, /g PRO 199, /g
ALA 237, /h LEU 120  
Chain-final residues that are actual C termini: /A GLN 251, /B ALA 249, /C ILE
244, /F ILE 234, /H ILE 148, /I ILE 249, /K PHE 195, /M ASP 241, /N LEU 215,
/O ILE 276, /P PHE 262, /Q GLU 248, /R GLN 251, /S ALA 249, /T ILE 244, /W ILE
234, /Y ILE 148, /Z ILE 249, /b PHE 195, /d ASP 241, /e LEU 215, /f ILE 276,
/g PHE 262, /h GLU 248  
Chain-final residues that are not actual C termini: /A PHE 186, /C LYS 218, /D
GLU 237, /D ARG 48, /D THR 60, /D VAL 202, /E GLU 247, /E GLY 126, /G ALA 243,
/G PRO 184, /G HIS 204, /H GLY 125, /I ASN 18, /I PRO 222, /J LYS 201, /J ASP
26, /J ALA 175, /K LYS 19, /K LEU 28, /K MET 174, /L HIS 264, /L VAL 92, /L
LYS 167, /L VAL 205, /M ASN 174, /O VAL 80, /O ALA 159, /P GLU 52, /P GLU 125,
/P PHE 145, /P LEU 193, /P GLN 231, /Q TYR 109, /R PHE 186, /T LYS 218, /U GLU
237, /U ARG 48, /U THR 60, /U VAL 202, /V GLU 247, /V GLY 126, /X ALA 243, /X
PRO 184, /X HIS 204, /Y GLY 125, /Z ASN 18, /Z PRO 222, /a LYS 201, /a ASP 26,
/a ALA 175, /b LYS 19, /b LEU 28, /b MET 174, /c HIS 264, /c VAL 92, /c LYS
167, /c VAL 205, /d ASN 174, /f VAL 80, /f ALA 159, /g GLU 52, /g GLU 125, /g
PHE 145, /g LEU 193, /g GLN 231, /h TYR 109  
5569 hydrogen bonds  
/D GLU 237 is not terminus, removing H atom from 'C'  
/E GLU 247 is not terminus, removing H atom from 'C'  
/G ALA 243 is not terminus, removing H atom from 'C'  
/J LYS 201 is not terminus, removing H atom from 'C'  
/L HIS 264 is not terminus, removing H atom from 'C'  
5 messages similar to the above omitted  
46 hydrogens added  


clipper associate #2 toModel #1

Opened preholo_3A_J319_C2_sharp.mrc as #1.1.1.1, grid size 360,360,360, pixel
1.06, shown at level 0.779, step 1, values float32  
Chain information for MwergedPDB-KKSP.pdb  
---  
Chain | Description  
1.2/A 1.2/R | No description available  
1.2/B 1.2/S | No description available  
1.2/C 1.2/T | No description available  
1.2/D 1.2/U | No description available  
1.2/E 1.2/V | No description available  
1.2/F 1.2/W | No description available  
1.2/G 1.2/X | No description available  
1.2/H 1.2/Y | No description available  
1.2/I 1.2/Z | No description available  
1.2/J 1.2/a | No description available  
1.2/K 1.2/b | No description available  
1.2/L 1.2/c | No description available  
1.2/M 1.2/d | No description available  
1.2/N 1.2/e | No description available  
1.2/O 1.2/f | No description available  
1.2/P 1.2/g | No description available  
1.2/Q 1.2/h | No description available  


isolde start

set selectionWidth 4

Done loading forcefield  
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 450.80.02
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            31G        8.5G        252M        272M         22G         22G
	Swap:          2.0G         61M        1.9G

Graphics:
	01:00.0 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"	defect	closed	moderate		Structure Editing		can't reproduce						all	ChimeraX