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#2972 closed defect (can't reproduce)

Weird problem reading Amber CMAP terms

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:        Darwin-19.3.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-12-23)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-12-23)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/zhoub2/Volumes/labmac/Temp/H14_Nuc197_scFv/cryosparc/cryosparc_P15_J426_class01_zflipped_densities_C_term.mrc

Opened cryosparc_P15_J426_class01_zflipped_densities_C_term.mrc, grid size
128,128,128, pixel 2.57, shown at level 0.641, step 1, values float32  

> volume #1 level 0.401

> set bgColor white

> lighting soft

> lighting full

> open
> "/Users/zhoub2/Volumes/labmac/Temp/H14_Nuc197_scFv/cryosparc/model_H3_23-36_from
> H14_Nuc197_rsr12_fit_into_P15_J426_zflipped_map-coot-1.pdb"

Chain information for model_H3_23-36_from
H14_Nuc197_rsr12_fit_into_P15_J426_zflipped_map-coot-1.pdb #2  
---  
Chain | Description  
E | No description available  
  

> close #2

> lighting full

> lighting full

> lighting simple

> lighting soft

> lighting full

> save /Users/zhoub2/NIH-
> OneDrive/Manuscript/LH_Nuc197/figures/model_maps/H14/H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities.mrc
> models #1

> open "/Users/zhoub2/OneDrive - National Institutes of
> Health/projects/H14_Nuc197_scFv/model_building/RealSpaceRefine_27/H14_Nuc197_2scFv_RSR23__add_H3_N-
> terminal_ISOLDE_adjusted.cif-coot-0_noH_real_space_refined.pdb"

Chain information for H14_Nuc197_2scFv_RSR23__add_H3_N-
terminal_ISOLDE_adjusted.cif-coot-0_noH_real_space_refined.pdb #2  
---  
Chain | Description  
A | No description available  
B F | No description available  
C G | No description available  
D | No description available  
E | No description available  
H | No description available  
I | No description available  
J | No description available  
M N | No description available  
U | No description available  
  

> hide #!1 models

> show #!1 models

> select #2

18496 atoms, 19652 bonds, 4 pseudobonds, 2 models selected  

> ~select #2

Nothing selected  

> show cartoons

> hide atoms

> fitmap #2 inMap #1

Fit molecule H14_Nuc197_2scFv_RSR23__add_H3_N-terminal_ISOLDE_adjusted.cif-
coot-0_noH_real_space_refined.pdb (#2) to map
H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities.mrc (#1)
using 18496 atoms  
average map value = 0.7776, steps = 104  
shifted from previous position = 9.75  
rotated from previous position = 12.1 degrees  
atoms outside contour = 8562, contour level = 0.40104  
  
Position of H14_Nuc197_2scFv_RSR23__add_H3_N-terminal_ISOLDE_adjusted.cif-
coot-0_noH_real_space_refined.pdb (#2) relative to
H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.98071664 0.08732293 0.17484160 -34.34348103  
-0.07348355 0.99374136 -0.08413255 28.32953947  
-0.18109403 0.06966221 0.98099548 29.38237967  
Axis 0.36638399 0.84794246 -0.38308792  
Axis point 140.35789750 0.00000000 212.28963295  
Rotation angle (degrees) 12.11543405  
Shift along axis 0.18288319  
  

> fitmap #2 inMap #1 search 100

Found 79 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (96 of 100).  
  
Average map values and times found:  
1.879 (4), 1.795 (3), 1.175 (2), 1.092 (1), 1.082 (2), 1.082 (2), 1.067 (1),
1.028 (1), 0.9028 (1), 0.8989 (1), 0.8163 (1), 0.7983 (2), 0.7756 (1), 0.7756
(1), 0.7754 (1), 0.7722 (3), 0.7706 (2), 0.7672 (1), 0.761 (1), 0.7593 (2),
0.7574 (1), 0.75 (1), 0.7488 (1), 0.7481 (2), 0.7469 (1), 0.7422 (1), 0.7386
(1), 0.7378 (1), 0.7358 (2), 0.7335 (1), 0.7316 (1), 0.7306 (1), 0.7301 (1),
0.7261 (1), 0.7255 (1), 0.7249 (1), 0.7248 (1), 0.7241 (1), 0.7221 (1), 0.7215
(1), 0.7203 (1), 0.7195 (1), 0.7183 (1), 0.7176 (1), 0.7174 (1), 0.7151 (2),
0.7131 (1), 0.7093 (1), 0.7091 (1), 0.7081 (1), 0.7058 (1), 0.7019 (1), 0.6972
(1), 0.695 (1), 0.6881 (1), 0.6877 (1), 0.6851 (1), 0.6845 (1), 0.6821 (1),
0.6619 (1), 0.654 (1), 0.6304 (1), 0.6235 (1), 0.6071 (1), 0.5924 (2), 0.5805
(1), 0.4918 (1), 0.413 (1), 0.405 (1), 0.3801 (1), 0.3779 (1), 0.3609 (1),
0.3524 (1), 0.3432 (1), 0.3379 (1), 0.2766 (1), 0.1977 (1), 0.1798 (1), 0.1563
(1)  
  
Best fit found:  
Fit molecule H14_Nuc197_2scFv_RSR23__add_H3_N-terminal_ISOLDE_adjusted.cif-
coot-0_noH_real_space_refined.pdb (#2) to map
H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities.mrc (#1)
using 18496 atoms  
average map value = 1.879, steps = 504  
shifted from previous position = 137  
rotated from previous position = 80.4 degrees  
atoms outside contour = 791, contour level = 0.40104  
Position of H14_Nuc197_2scFv_RSR23__add_H3_N-terminal_ISOLDE_adjusted.cif-
coot-0_noH_real_space_refined.pdb (#2) relative to
H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99995439 -0.00366137 0.00882746 2.79881370  
-0.00354715 -0.99991023 -0.01292298 328.73698988  
0.00887397 0.01289105 -0.99987756 318.65079613  
Axis 0.99998859 -0.00180203 0.00442468  
Axis point 0.00000000 163.34279437 160.38004886  
Rotation angle (degrees) 179.26045350  
Shift along axis 3.61631693  
  
Found 79 fits. List window not yet implemented.  

> volume #1 level 0.7543

> fitmap #2 inMap #1 search 10

Found 10 unique fits from 10 random placements having fraction of points
inside contour >= 0.100 (10 of 10).  
  
Average map values and times found:  
1.879 (1), 1.068 (1), 0.7853 (1), 0.7491 (1), 0.7255 (1), 0.7232 (1), 0.709
(1), 0.6668 (1), 0.6493 (1), 0.6296 (1)  
  
Best fit found:  
Fit molecule H14_Nuc197_2scFv_RSR23__add_H3_N-terminal_ISOLDE_adjusted.cif-
coot-0_noH_real_space_refined.pdb (#2) to map
H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities.mrc (#1)
using 18496 atoms  
average map value = 1.879, steps = 340  
shifted from previous position = 95.1  
rotated from previous position = 56.6 degrees  
atoms outside contour = 2099, contour level = 0.75429  
Position of H14_Nuc197_2scFv_RSR23__add_H3_N-terminal_ISOLDE_adjusted.cif-
coot-0_noH_real_space_refined.pdb (#2) relative to
H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99995279 -0.00358678 0.00903739 2.75459676  
-0.00347346 -0.99991550 -0.01252746 328.67599787  
0.00908156 0.01249546 -0.99988072 318.68918884  
Axis 0.99998819 -0.00176511 0.00452855  
Axis point 0.00000000 163.34360188 160.36649593  
Rotation angle (degrees) 179.28311891  
Shift along axis 3.61761342  
  
Found 10 fits. List window not yet implemented.  

> close #2

> close #1

> open "/Users/zhoub2/OneDrive - National Institutes of
> Health/Manuscript/LH_Nuc197/figures/model_maps/H14/H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities_2.52angpix.mrc"

Opened
H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities_2.52angpix.mrc,
grid size 128,128,128, pixel 2.52, shown at level 0.641, step 1, values
float32  

> volume #1 level 0.3253

> open "/Users/zhoub2/OneDrive - National Institutes of
> Health/Manuscript/LH_Nuc197/figures/model_maps/H14/H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities_2.52angpix-
> coot-add_H14_C-terminal.pdb"

Chain information for
H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities_2.52angpix-
coot-add_H14_C-terminal.pdb #2  
---  
Chain | Description  
A | No description available  
B F | No description available  
C G | No description available  
D | No description available  
E | No description available  
H | No description available  
I | No description available  
J | No description available  
M N | No description available  
U | No description available  
  

> volume #1 level 0.237

> volume #1 level 0.338

> style stick

Changed 18576 atom styles  

> volume #1 level 0.401

> hide #!2 models

> show #!2 models

> lighting full

> lighting simple

> color /I,J #DDCAB9

> color /D,H #F4CACB

> color /C,G #FFF104

> color /A,E #6994CE

> color /B,F #7FCA9C

> color /M,N light grey

Unknown command: (d3d3d3);10  

> color #3/U #33376D

> color /U #33376D

> color zone #1 near #2/U distance 2

> color zone #1 near #2/U distance 5

> hide #!2 models

> lighting soft

> lighting full

> lighting soft

> show #!2 models

> hide #!2 models

> show #!2 models

> show cartoons

> hide atoms

Unknown command: addH  

> addh

Summary of feedback from adding hydrogens to
H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities_2.52angpix-
coot-add_H14_C-terminal.pdb #2  
---  
notes | No usable SEQRES records for
H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities_2.52angpix-
coot-add_H14_C-terminal.pdb (#2) chain A; guessing termini instead  
No usable SEQRES records for
H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities_2.52angpix-
coot-add_H14_C-terminal.pdb (#2) chain B; guessing termini instead  
No usable SEQRES records for
H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities_2.52angpix-
coot-add_H14_C-terminal.pdb (#2) chain C; guessing termini instead  
No usable SEQRES records for
H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities_2.52angpix-
coot-add_H14_C-terminal.pdb (#2) chain D; guessing termini instead  
No usable SEQRES records for
H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities_2.52angpix-
coot-add_H14_C-terminal.pdb (#2) chain E; guessing termini instead  
8 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A LYS 23, /B LYS 20, /C ALA
10, /D LYS 27, /E LYS 23, /F LYS 20, /G ALA 10, /H LYS 27, /I DG 1, /J DG 1,
/M GLU 23, /N GLU 23, /U SER 35  
Chain-initial residues that are not actual N termini: /M GLY 156, /N GLY 156  
Chain-final residues that are actual C termini: /A ALA 135, /B GLY 102, /F GLY
102, /H LYS 122, /I DC 197, /J DC 197  
Chain-final residues that are not actual C termini: /C LYS 118, /D ALA 121, /E
ARG 134, /G LYS 118, /M LYS 265, /M SER 141, /N LYS 265, /N SER 141, /U ALA
125  
1863 hydrogen bonds  
Adding 'H' to /M GLY 156  
Adding 'H' to /N GLY 156  
/C LYS 118 is not terminus, removing H atom from 'C'  
/D ALA 121 is not terminus, removing H atom from 'C'  
/E ARG 134 is not terminus, removing H atom from 'C'  
/G LYS 118 is not terminus, removing H atom from 'C'  
/M LYS 265 is not terminus, removing H atom from 'C'  
4 messages similar to the above omitted  
15269 hydrogens added  
  

> hide HC

> hide #!1 models

> show #!1 models

> clipper associate #1 toModel #2

Chain information for
H14_Nuc197_cryosparc_P15_J426_class01_zflipped_H14-C-Term_densities_2.52angpix-
coot-add_H14_C-terminal.pdb  
---  
Chain | Description  
1.1/A | No description available  
1.1/B 1.1/F | No description available  
1.1/C 1.1/G | No description available  
1.1/D | No description available  
1.1/E | No description available  
1.1/H | No description available  
1.1/I | No description available  
1.1/J | No description available  
1.1/M 1.1/N | No description available  
1.1/U | No description available  
  

Unknown command: isolde start2  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> select #2/U:109-125

Nothing selected  

> select /U:109-125

182 atoms, 181 bonds, 1 model selected  

Unknown command: solde restrain distances sel  

Unknown command: solde restrain distances /U:109-125  

> isolde restrain distances /U:109-125

> isolde sim start sel

Traceback (most recent call last):  
File
"/Users/zhoub2/dev/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/Users/zhoub2/dev/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/cmd.py", line 77, in isolde_sim  
isolde.start_sim()  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 2696, in start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 613, in __init__  
self._initialize_restraints(uh)  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 759, in
_initialize_restraints  
sh.initialize_restraint_forces(amber_cmap)  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1470, in
initialize_restraint_forces  
self.initialize_amber_cmap_force()  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1802, in
initialize_amber_cmap_force  
from .custom_forces import AmberCMAPForce  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 74, in <module>  
class AmberCMAPForce(CMAPTorsionForce):  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 80, in AmberCMAPForce  
_map_loader = amber_cmap.CMAPLoader()  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/amber_cmap.py", line 64, in __init__  
self._load_maps()  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/amber_cmap.py", line 108, in _load_maps  
self._maps.append(self._load_map(name))  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/amber_cmap.py", line 93, in _load_map  
alpha = (numpy.loadtxt(os.path.join(basedir, '{}_alpha.txt'.format(stem))) *  
File
"/Users/zhoub2/dev/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/npyio.py", line 968, in loadtxt  
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)  
File
"/Users/zhoub2/dev/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/_datasource.py", line 268, in open  
ds = DataSource(destpath)  
File
"/Users/zhoub2/dev/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/_datasource.py", line 325, in __init__  
self._destpath = os.path.abspath(destpath)  
File
"/Users/zhoub2/dev/Applications/ChimeraX-0.91.app/Contents/bin/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 383, in abspath  
cwd = os.getcwd()  
OSError: [Errno 6] Device not configured  
  
OSError: [Errno 6] Device not configured  
  
File
"/Users/zhoub2/dev/Applications/ChimeraX-0.91.app/Contents/bin/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 383, in abspath  
cwd = os.getcwd()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 2676, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/isolde.py", line 2696, in start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 613, in __init__  
self._initialize_restraints(uh)  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 759, in
_initialize_restraints  
sh.initialize_restraint_forces(amber_cmap)  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1470, in
initialize_restraint_forces  
self.initialize_amber_cmap_force()  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1802, in
initialize_amber_cmap_force  
from .custom_forces import AmberCMAPForce  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 74, in <module>  
class AmberCMAPForce(CMAPTorsionForce):  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 80, in AmberCMAPForce  
_map_loader = amber_cmap.CMAPLoader()  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/amber_cmap.py", line 64, in __init__  
self._load_maps()  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/amber_cmap.py", line 108, in _load_maps  
self._maps.append(self._load_map(name))  
File "/Users/zhoub2/Library/Application Support/ChimeraX/0.91/site-
packages/chimerax/isolde/openmm/amber_cmap.py", line 93, in _load_map  
alpha = (numpy.loadtxt(os.path.join(basedir, '{}_alpha.txt'.format(stem))) *  
File
"/Users/zhoub2/dev/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/npyio.py", line 968, in loadtxt  
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)  
File
"/Users/zhoub2/dev/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/_datasource.py", line 268, in open  
ds = DataSource(destpath)  
File
"/Users/zhoub2/dev/Applications/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/numpy/lib/_datasource.py", line 325, in __init__  
self._destpath = os.path.abspath(destpath)  
File
"/Users/zhoub2/dev/Applications/ChimeraX-0.91.app/Contents/bin/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 383, in abspath  
cwd = os.getcwd()  
OSError: [Errno 6] Device not configured  
  
OSError: [Errno 6] Device not configured  
  
File
"/Users/zhoub2/dev/Applications/ChimeraX-0.91.app/Contents/bin/../Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/posixpath.py",
line 383, in abspath  
cwd = os.getcwd()  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.5.5
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (4)

comment:1 by Eric Pettersen, 6 years ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Weird problem reading Amber CMAP terms

in reply to: 2 ; follow-up: 2 comment:2 by Tristan Croll, 6 years ago

... huh? I have no idea what to say about that. Literally all it’s doing there is opening a text file.

in reply to: 3 ; follow-up: 3 comment:3 by Tristan Croll, 6 years ago

Looks like it may be this (sshfs connection not waking properly after 
sleep)? https://github.com/osxfuse/osxfuse/issues/45

On 2020-03-24 05:54, ChimeraX wrote:

comment:4 by Tristan Croll, 6 years ago

Resolution:	→ can't reproduce
Status:	assigned → closed

Don't think this has anything to do with ISOLDE per se. Just looks like a system I/O error that happened to manifest when ISOLDE was trying to read a file.

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