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Opened 6 years ago
Closed 3 years ago
#2424 closed defect (fixed)
Array of coordinates is None
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted: Platform: Linux-3.10.0-957.21.3.el7.x86_64-x86_64-with-centos-7.6.1810-Core ChimeraX Version: 0.91 (2019-08-27) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-08-27) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > select up Nothing selected > isolde start > set selectionWidth 4 Done loading forcefield > open 6eyd 6eyd title: Structure of Mycobacterium smegmatis RNA polymerase Sigma-A holoenzyme [more info...] Chain information for 6eyd #1 --- Chain | Description A B | DNA-directed RNA polymerase subunit α C | DNA-directed RNA polymerase subunit β D | DNA-directed RNA polymerase subunit beta' E | DNA-directed RNA polymerase subunit ω F | RNA polymerase σ factor SigA Non-standard residues in 6eyd #1 --- MG — magnesium ion ZN — zinc ion 6eyd title: Structure of Mycobacterium smegmatis RNA polymerase Sigma-A holoenzyme [more info...] Chain information for 6eyd --- Chain | Description 1.3/A 1.3/B | DNA-directed RNA polymerase subunit α 1.3/C | DNA-directed RNA polymerase subunit β 1.3/D | DNA-directed RNA polymerase subunit beta' 1.3/E | DNA-directed RNA polymerase subunit ω 1.3/F | RNA polymerase σ factor SigA Non-standard residues in 6eyd #1.3 --- MG — magnesium ion ZN — zinc ion > open 3983 fromDatabase emdb Opened emd_3983.map, grid size 208,208,208, pixel 1.34, shown at level 0.0941, step 1, values float32 > set bgColor white > fitmap #1 inMap #2 moveWholeMolecules false Fit molecule 6eyd (#1.3) to map 3983 (#2) using 22931 atoms average map value = 0.1364, steps = 48 shifted from previous position = 0.0209 rotated from previous position = 0.0122 degrees atoms outside contour = 17203, contour level = 0.17637 > clipper associate #2 toModel #1 > select clear > clipper spotlight radius 13.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 14.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 15.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 16.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 17.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 18.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 17.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 16.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 15.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 14.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 13.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 12.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 11.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 12.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 13.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 14.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 15.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 16.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 17.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 18.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 19.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 20.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 21.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 22.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 23.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 24.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 25.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 24.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 23.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 22.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 21.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 20.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 19.00 Setting spotlight mode for model 1.3 to True > clipper spotlight radius 18.00 Setting spotlight mode for model 1.3 to True > close before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb #1 --- Chain | Description A | predicted microcompartment protein before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb --- Chain | Description 1.3/A | predicted microcompartment protein WARNING: multiple experimental reflection datasets found: (dataset) FOBS, SIGFOBS, (dataset) IOBS, SIGIOBS, (dataset) DANO, SIGDANO, (dataset) F(+), SIGF(+), F(-), SIGF(-), (dataset) I(+), SIGI(+), I(-), SIGI(-) Automatically choosing "(dataset) IOBS, SIGIOBS". Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... > set bgColor white > set bgColor gray > set bgColor black > set bgColor gray > set bgColor white > set bgColor gray > hide HC > hide H > show H > hide H > show HC > hide H Unknown command: addH true > show H > hide HC > select clear QWidget::repaint: Recursive repaint detected > select clear > select clear > select clear > select clear > select up 17 atoms, 16 bonds, 1 model selected > select up 176 atoms, 178 bonds, 1 model selected > select up 3348 atoms, 3371 bonds, 1 model selected > select clear > select clear > select clear > select clear > select clear > select clear > select clear > select clear > select clear > select clear > select clear > select clear > select clear > select clear > select up 91 atoms, 90 bonds, 1 model selected > select up 3348 atoms, 3371 bonds, 1 model selected clipper isolate Missing or invalid "atoms" argument: empty atom specifier > select clear > select up 12 atoms, 11 bonds, 1 model selected > select up 332 atoms, 332 bonds, 1 model selected > select clear > select clear > select clear clipper isolate Missing or invalid "atoms" argument: empty atom specifier clipper isolate Missing or invalid "atoms" argument: empty atom specifier Traceback (most recent call last): File "/usr/mbu/software/chimerax/chimerax-2019.08.27/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/ym337/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 1650, in _push_coords_to_sim self.thread_handler.coords = self._pending_coords File "/home/ym337/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 309, in coords f(self._c_pointer, n, pointer(coords)) File "/usr/mbu/software/chimerax/chimerax-2019.08.27/lib/python3.7/site- packages/chimerax/atomic/molc.py", line 320, in pointer cty = numpy_type_to_ctype[a.dtype.type] AttributeError: 'NoneType' object has no attribute 'dtype' Error processing trigger "coord update": AttributeError: 'NoneType' object has no attribute 'dtype' File "/usr/mbu/software/chimerax/chimerax-2019.08.27/lib/python3.7/site- packages/chimerax/atomic/molc.py", line 320, in pointer cty = numpy_type_to_ctype[a.dtype.type] See log for complete Python traceback. Traceback (most recent call last): File "/usr/mbu/software/chimerax/chimerax-2019.08.27/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/ym337/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 1650, in _push_coords_to_sim self.thread_handler.coords = self._pending_coords File "/home/ym337/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 309, in coords f(self._c_pointer, n, pointer(coords)) File "/usr/mbu/software/chimerax/chimerax-2019.08.27/lib/python3.7/site- packages/chimerax/atomic/molc.py", line 320, in pointer cty = numpy_type_to_ctype[a.dtype.type] AttributeError: 'NoneType' object has no attribute 'dtype' Error processing trigger "coord update": AttributeError: 'NoneType' object has no attribute 'dtype' File "/usr/mbu/software/chimerax/chimerax-2019.08.27/lib/python3.7/site- packages/chimerax/atomic/molc.py", line 320, in pointer cty = numpy_type_to_ctype[a.dtype.type] See log for complete Python traceback. [_many_ of these deleted] Traceback (most recent call last): File "/usr/mbu/software/chimerax/chimerax-2019.08.27/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/ym337/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 1650, in _push_coords_to_sim self.thread_handler.coords = self._pending_coords File "/home/ym337/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 309, in coords f(self._c_pointer, n, pointer(coords)) File "/usr/mbu/software/chimerax/chimerax-2019.08.27/lib/python3.7/site- packages/chimerax/atomic/molc.py", line 320, in pointer cty = numpy_type_to_ctype[a.dtype.type] AttributeError: 'NoneType' object has no attribute 'dtype' Error processing trigger "coord update": AttributeError: 'NoneType' object has no attribute 'dtype' File "/usr/mbu/software/chimerax/chimerax-2019.08.27/lib/python3.7/site- packages/chimerax/atomic/molc.py", line 320, in pointer cty = numpy_type_to_ctype[a.dtype.type] See log for complete Python traceback. Traceback (most recent call last): File "/usr/mbu/software/chimerax/chimerax-2019.08.27/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/home/ym337/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 1650, in _push_coords_to_sim self.thread_handler.coords = self._pending_coords File "/home/ym337/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 309, in coords f(self._c_pointer, n, pointer(coords)) File "/usr/mbu/software/chimerax/chimerax-2019.08.27/lib/python3.7/site- packages/chimerax/atomic/molc.py", line 320, in pointer cty = numpy_type_to_ctype[a.dtype.type] AttributeError: 'NoneType' object has no attribute 'dtype' Error processing trigger "coord update": AttributeError: 'NoneType' object has no attribute 'dtype' File "/usr/mbu/software/chimerax/chimerax-2019.08.27/lib/python3.7/site- packages/chimerax/atomic/molc.py", line 320, in pointer cty = numpy_type_to_ctype[a.dtype.type] See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 418.67 OpenGL renderer: GeForce GTX 1080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (3)
comment:1 by , 6 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Array of coordinates is None |
comment:3 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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