ISOLDE/OpenMM: Invoked getPositions() on a State which does not contain positions

[jliu321@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.12.1.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.9 (2019-06-06)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /data2/users/jliu/ccpem_project/Flex-EM_3/1_MD/final1_mdcg.pdb

Chain information for final1_mdcg.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open /data2/users/jliu/Documents/J79/J79_map_invert.mrc

Opened J79_map_invert.mrc, grid size 288,288,288, pixel 1.06, shown at level
0.294, step 2, values float32  

> ui mousemode rightMode "rotate selected models"

> select #1

10404 atoms, 10542 bonds selected  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> fitmap #1 inMap #2

Fit molecule final1_mdcg.pdb (#1) to map J79_map_invert.mrc (#2) using 10404
atoms  
average map value = 0.4909, steps = 116  
shifted from previous position = 9.65  
rotated from previous position = 6.16 degrees  
atoms outside contour = 3741, contour level = 0.29422  
  
Position of final1_mdcg.pdb (#1) relative to J79_map_invert.mrc (#2)
coordinates:  
Matrix rotation and translation  
-0.96239600 -0.04256905 0.26829437 274.52001913  
-0.17241686 -0.66748987 -0.72438233 356.81491917  
0.20992005 -0.74340112 0.63504992 133.05039824  
Axis -0.13241463 0.40642003 -0.90404044  
Axis point 134.70529547 202.88620204 0.00000000  
Rotation angle (degrees) 175.88174344  
Shift along axis -11.61667520  
  

> addh

Summary of feedback from adding hydrogens to final1_mdcg.pdb #1  
---  
warning | Unknown hybridization for atoms (C8, C3, C4, O4, C1, C7, O3, O6, C5,
O5, C6, O7, C2) of residue type NAG; not adding hydrogens to them  
notes | No usable SEQRES records for final1_mdcg.pdb (#1) chain A; guessing
termini instead  
No usable SEQRES records for final1_mdcg.pdb (#1) chain B; guessing termini
instead  
No usable SEQRES records for final1_mdcg.pdb (#1) chain C; guessing termini
instead  
No usable SEQRES records for final1_mdcg.pdb (#1) chain D; guessing termini
instead  
No usable SEQRES records for final1_mdcg.pdb (#1) chain E; guessing termini
instead  
Chain-initial residues that are actual N termini: /A GLU 190, /B PRO 37, /C
GLN 1, /D LYS 289, /E LEU 40  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 287, /B GLN 273, /C SER
189, /D GLN 389, /E ALA 713  
Chain-final residues that are not actual C termini:  
676 hydrogen bonds  
10265 hydrogens added  
  

> show selAtoms

> hide selAtoms

> hide selAtoms

> show selAtoms ribbons

> hide selAtoms

> show selAtoms

> hide selAtoms

> hide

> hide HC

> toolshed show ISOLDE

> set selectionWidth 4

Chain information for final1_mdcg.pdb  
---  
Chain | Description  
1.3/A | No description available  
1.3/B | No description available  
1.3/C | No description available  
1.3/D | No description available  
1.3/E | No description available  
  
Done loading forcefield  

> select #1.3.1

2 models selected  

> select #1.3.2

2 models selected  

> ~select #1.3.3

2 models selected  

> ~select #1.3

Nothing selected  

> select #1

20669 atoms, 20807 bonds, 7 models selected  

> hide #!2 models

> hide #!2.1 models

> hide #!1.3.1 models

> hide #!1.3.2 models

> hide #!1.3.3 models

> hide #!1.1 models

> show #!1.2 models

> hide #!1 models

> show #!1 models

> hide #!1.3 models

> show #!1.3 models

> select #1.3

20669 atoms, 20807 bonds, 5 models selected  

> clipper associate #2 toModel #1.3

> clipper spotlight radius 20.00

Setting spotlight mode for model 1.3 to True  

> clipper spotlight radius 20.00

Setting spotlight mode for model 1.3 to True  

> clipper associate #2 toModel #1.3

Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/delayed_reaction.py", line 65, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1552, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 301, in coords  
f(self._c_pointer, n, pointer(coords))  
RuntimeError: Invoked getPositions() on a State which does not contain
positions.  
  
Error processing trigger "new frame": Invoked getPositions() on a State which
does not contain positions.:  
RuntimeError: Invoked getPositions() on a State which does not contain
positions.  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 301, in coords  
f(self._c_pointer, n, pointer(coords))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 410.79
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[pett]

duplicate of #2650