id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6237 Problem switching GPU sergei.gurianov@… Tristan Croll "The following bug report has been submitted: Platform: Windows-10-10.0.19042 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description In ISOLDE tool tried to switch from Intel graphics to Nvidia to run MD on dedicated graphics processor on a laptop with Nvidia Optimus using command 'isolde set gpuDeviceIndex 0'. Any but '-1' integer value result in same error: openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. Tried to change settings in Nvidia utility to utilise Nvidia GPU wherever possible with no success in changing GPU for MD simulation. 3D rendering could be directed to Nvidia though. CUDA is not installed, just latest video driver. Log: Startup Messages --- warning | Registration file 'C:\\\Users\\\segurian\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\registration' has expired UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX open C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\demo_data\6out\6out.pdb format pdb 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb #1 --- Chain | Description | UniProt A | capsid protein VP1 | CAPSD_NVN68 B | capsid protein VP1 | CAPSD_NVN68 C | capsid protein VP1 | CAPSD_NVN68 open 20205 format ccp4 fromDatabase emdb Opened emdb 20205 as #2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at level 0.287, step 1, values float32 clipper associate #2 toModel #1 Opened emdb 20205 as #1.1.1.1, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at level 0.168, step 1, values float32 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb --- Chain | Description | UniProt 1.2/A | capsid protein VP1 | CAPSD_NVN68 1.2/B | capsid protein VP1 | CAPSD_NVN68 1.2/C | capsid protein VP1 | CAPSD_NVN68 addh Summary of feedback from adding hydrogens to 6out.pdb #1.2 --- notes | No usable SEQRES records for 6out.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for 6out.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for 6out.pdb (#1.2) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A ASP 29, /B THR 9, /C ASP 29 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A SER 520, /B ALA 519, /C ALA 519 1438 hydrogen bonds /A SER 520 is not terminus, removing H atom from 'C' /B ALA 519 is not terminus, removing H atom from 'C' /C ALA 519 is not terminus, removing H atom from 'C' 11443 hydrogens added isolde start set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 51 residues in model #1.2 to IUPAC-IUB standards. Done loading forcefield set bgColor white ISOLDE: started sim reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim isolde set gpuDeviceIndex 0 Traceback (most recent call last): File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2749, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2804, in start_sim sm.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1606, in start_sim self._prepare_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1564, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\openmm\app\simulation.py"", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. isolde set gpuDeviceIndex 1 Traceback (most recent call last): File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2749, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2804, in start_sim sm.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1606, in start_sim self._prepare_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1564, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\openmm\app\simulation.py"", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1168, in _dihe_r_changed_cb self.sim_handler.update_dihedral_restraints(all_changeds) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1975, in update_dihedral_restraints force.update_targets(restraints.sim_indices, File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range Error processing trigger ""changes"": RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) See log for complete Python traceback. isolde set gpuDeviceIndex 2 Traceback (most recent call last): File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2749, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2804, in start_sim sm.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1606, in start_sim self._prepare_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1564, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\openmm\app\simulation.py"", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. select clear ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim Traceback (most recent call last): File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2749, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2804, in start_sim sm.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1606, in start_sim self._prepare_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1564, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\openmm\app\simulation.py"", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. isolde set gpuDeviceIndex -1 ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim isolde set gpuDeviceIndex NVIDIA Invalid ""gpuDeviceIndex"" argument: Expected an integer isolde set gpuDeviceIndex 3 Traceback (most recent call last): File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2749, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2804, in start_sim sm.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1606, in start_sim self._prepare_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1564, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\openmm\app\simulation.py"", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. isolde set gpuDeviceIndex -2 Traceback (most recent call last): File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2749, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2804, in start_sim sm.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1606, in start_sim self._prepare_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1564, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\openmm\app\simulation.py"", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. isolde set gpuDeviceIndex -1 ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim isolde set gpuDeviceIndex -2 Traceback (most recent call last): File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2749, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2804, in start_sim sm.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1606, in start_sim self._prepare_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1564, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\openmm\app\simulation.py"", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. isolde set gpuDeviceIndex -3 Traceback (most recent call last): File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2749, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2804, in start_sim sm.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1606, in start_sim self._prepare_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1564, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\openmm\app\simulation.py"", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. isolde set gpuDeviceIndex 4 Traceback (most recent call last): File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2749, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2804, in start_sim sm.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1606, in start_sim self._prepare_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1564, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\openmm\app\simulation.py"", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim Traceback (most recent call last): File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2749, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2804, in start_sim sm.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1606, in start_sim self._prepare_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1564, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\openmm\app\simulation.py"", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1168, in _dihe_r_changed_cb self.sim_handler.update_dihedral_restraints(all_changeds) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1975, in update_dihedral_restraints force.update_targets(restraints.sim_indices, File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range Error processing trigger ""changes"": RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) See log for complete Python traceback. isolde set gpuDeviceIndex -1 ISOLDE: started sim ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim isolde set gpuDeviceIndex 1 Traceback (most recent call last): File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2749, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\isolde.py"", line 2804, in start_sim sm.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1606, in start_sim self._prepare_sim() File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1564, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\openmm\app\simulation.py"", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py"", line 4605, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1168, in _dihe_r_changed_cb self.sim_handler.update_dihedral_restraints(all_changeds) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1975, in update_dihedral_restraints force.update_targets(restraints.sim_indices, File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range Error processing trigger ""changes"": RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1168, in _dihe_r_changed_cb self.sim_handler.update_dihedral_restraints(all_changeds) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1975, in update_dihedral_restraints force.update_targets(restraints.sim_indices, File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range Error processing trigger ""changes"": RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1168, in _dihe_r_changed_cb self.sim_handler.update_dihedral_restraints(all_changeds) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1975, in update_dihedral_restraints force.update_targets(restraints.sim_indices, File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range Error processing trigger ""changes"": RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1168, in _dihe_r_changed_cb self.sim_handler.update_dihedral_restraints(all_changeds) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1975, in update_dihedral_restraints force.update_targets(restraints.sim_indices, File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range Error processing trigger ""changes"": RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) See log for complete Python traceback. isolde set gpuDeviceIndex -1 ISOLDE: started sim Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1168, in _dihe_r_changed_cb self.sim_handler.update_dihedral_restraints(all_changeds) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1975, in update_dihedral_restraints force.update_targets(restraints.sim_indices, File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range Error processing trigger ""changes"": RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1168, in _dihe_r_changed_cb self.sim_handler.update_dihedral_restraints(all_changeds) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1975, in update_dihedral_restraints force.update_targets(restraints.sim_indices, File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range Error processing trigger ""changes"": RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1168, in _dihe_r_changed_cb self.sim_handler.update_dihedral_restraints(all_changeds) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1975, in update_dihedral_restraints force.update_targets(restraints.sim_indices, File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range Error processing trigger ""changes"": RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1168, in _dihe_r_changed_cb self.sim_handler.update_dihedral_restraints(all_changeds) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1975, in update_dihedral_restraints force.update_targets(restraints.sim_indices, File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range Error processing trigger ""changes"": RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1168, in _dihe_r_changed_cb self.sim_handler.update_dihedral_restraints(all_changeds) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1975, in update_dihedral_restraints force.update_targets(restraints.sim_indices, File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range Error processing trigger ""changes"": RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1168, in _dihe_r_changed_cb self.sim_handler.update_dihedral_restraints(all_changeds) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1975, in update_dihedral_restraints force.update_targets(restraints.sim_indices, File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range Error processing trigger ""changes"": RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1168, in _dihe_r_changed_cb self.sim_handler.update_dihedral_restraints(all_changeds) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1975, in update_dihedral_restraints force.update_targets(restraints.sim_indices, File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range Error processing trigger ""changes"": RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1168, in _dihe_r_changed_cb self.sim_handler.update_dihedral_restraints(all_changeds) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1975, in update_dihedral_restraints force.update_targets(restraints.sim_indices, File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range Error processing trigger ""changes"": RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1168, in _dihe_r_changed_cb self.sim_handler.update_dihedral_restraints(all_changeds) File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1975, in update_dihedral_restraints force.update_targets(restraints.sim_indices, File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range Error processing trigger ""changes"": RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range File ""C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\isolde\openmm\custom_forces.py"", line 1371, in update_targets f(int(self.this), n, pointer(ind), pointer(params)) See log for complete Python traceback. ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim ISOLDE: started sim OpenGL version: 3.3.0 NVIDIA 472.42 OpenGL renderer: NVIDIA GeForce MX150/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: LENOVO Model: 20L6SBKX00 OS: Microsoft Windows 10 Enterprise (Build 19042) Memory: 34,227,970,048 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz OSLanguage: en-US Locale: ('ru_RU', 'cp1252') 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: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-Clipper: 0.17.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 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: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.3 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 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: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 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: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 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: 0.4.4 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.2.0 parso: 0.8.3 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pywin32: 228 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 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: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 WMI: 1.5.1" defect assigned moderate Third Party all ChimeraX