Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5042 closed defect (fixed)

os.getcwd() failure saving map

Reported by: irina.grishkovskaya@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
problem occur whille saving mrc file, no problem with the saving pdb
Traceback (most recent call last):
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/save_command/dialog.py", line 116, in <lambda>
    lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file",
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
    _dlg.display(session, **kw)
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/save_command/dialog.py", line 51, in display
    run(session, cmd)
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/run.py", line 36, in run
    results = command.run(text, log=log, return_json=return_json)
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852, in run
    result = ci.function(session, **kw_args)
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/save_command/cmd.py", line 75, in cmd_save
    Command(session, registry=registry).run(provider_cmd_text, log=log)
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852, in run
    result = ci.function(session, **kw_args)
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/save_command/cmd.py", line 87, in provider_save
    provider_info.bundle_info.run_provider(session, provider_info.format_name,
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/map/__init__.py", line 164, in save
    save_map(session, path, _name, **kw)
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/map/volume.py", line 3974, in save_map
    save_grid_data(grids, path, session, format_name, options)
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/map_data/fileformats.py", line 297, in save_grid_data
    if matching_grid_path(glist, path):
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/map_data/fileformats.py", line 340, in matching_grid_path
    if realpath(gp) == rp:
  File "/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py", line 392, in realpath
    return abspath(path)
  File "/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py", line 379, in abspath
    cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory

FileNotFoundError: [Errno 2] No such file or directory

File "/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py", line 379, in abspath
cwd = os.getcwd()

See log for complete Python traceback.

/Users/irina.grishkovskaya/DRG1/Bud20/Krios/210812_Buds20_J2263/cryosparc_P144_J2263_flip.mrc models #2
Unknown command: /Users/irina.grishkovskaya/DRG1/Bud20/Krios/210812_Buds20_J2263/cryosparc_P144_J2263_flip.mrc models #2
save /Users/irina.grishkovskaya/DRG1/Bud20/Krios/210812_Buds20_J2263/cryosparc_P144_J2263_flip.mrc models #2Traceback (most recent call last):
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/cmd_line/tool.py", line 280, in execute
    cmd.run(cmd_text)
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852, in run
    result = ci.function(session, **kw_args)
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/save_command/cmd.py", line 75, in cmd_save
    Command(session, registry=registry).run(provider_cmd_text, log=log)
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852, in run
    result = ci.function(session, **kw_args)
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/save_command/cmd.py", line 87, in provider_save
    provider_info.bundle_info.run_provider(session, provider_info.format_name,
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/map/__init__.py", line 164, in save
    save_map(session, path, _name, **kw)
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/map/volume.py", line 3974, in save_map
    save_grid_data(grids, path, session, format_name, options)
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/map_data/fileformats.py", line 297, in save_grid_data
    if matching_grid_path(glist, path):
  File "/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/map_data/fileformats.py", line 340, in matching_grid_path
    if realpath(gp) == rp:
  File "/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py", line 392, in realpath
    return abspath(path)
  File "/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py", line 379, in abspath
    cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory

FileNotFoundError: [Errno 2] No such file or directory

File "/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py", line 379, in abspath
cwd = os.getcwd()

See log for complete Python traceback.


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
> /Users/irina.grishkovskaya/Downloads/cryosparc_P144_J2263_002_volume_map.mrc

Opened cryosparc_P144_J2263_002_volume_map.mrc as #1, grid size 480,480,480,
pixel 1.38, shown at level 0.263, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.2015

> volume flip #1 axis z

Opened cryosparc_P144_J2263_002_volume_map.mrc z flip as #2, grid size
480,480,480, pixel 1.38, shown at step 1, values float32  

> volume #1 level 0.1625

> volume #1 level 0.2841

> volume #1 level 0.4057

> set bgColor white

> save
> /Users/irina.grishkovskaya/DRG1/Bud20/Krios/cryosparc_P144_J2263_flip.mrc
> models #2

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/__init__.py", line 164, in save  
save_map(session, path, _name, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 3974, in save_map  
save_grid_data(grids, path, session, format_name, options)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_data/fileformats.py", line 297, in save_grid_data  
if matching_grid_path(glist, path):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_data/fileformats.py", line 340, in matching_grid_path  
if realpath(gp) == rp:  
File
"/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py",
line 392, in realpath  
return abspath(path)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py",
line 379, in abspath  
cwd = os.getcwd()  
FileNotFoundError: [Errno 2] No such file or directory  
  
FileNotFoundError: [Errno 2] No such file or directory  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py",
line 379, in abspath  
cwd = os.getcwd()  
  
See log for complete Python traceback.  
  

> open
> /Users/irina.grishkovskaya/DRG1/Bud20/Krios/deepEMhancer_results/210803_coordinates/2108046n8k_widetargetDEv1in-
> coot-18.pdb

Summary of feedback from opening
/Users/irina.grishkovskaya/DRG1/Bud20/Krios/deepEMhancer_results/210803_coordinates/2108046n8k_widetargetDEv1in-
coot-18.pdb  
---  
warnings | End residue of secondary structure not found: HELIX 7 7 UNK s 170
UNK s 179 1 10  
Start residue of secondary structure not found: HELIX 8 8 UNK s 181 UNK s 184
1 4  
Start residue of secondary structure not found: HELIX 44 44 LEU b 358 LYS b
360 1 3  
End residue of secondary structure not found: HELIX 117 117 GLU I 115 THR I
130 1 16  
Start residue of secondary structure not found: HELIX 239 239 SER y 231 GLU y
242 1 12  
  
Chain information for 2108046n8k_widetargetDEv1in-coot-18.pdb #3  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
u | No description available  
v | No description available  
y | No description available  
z | No description available  
  

> hide atoms

> show cartoons

> transparency 50

> volume #1 level 0.3133

> volume #1 level 0.01665

> volume #1 level 0.05

> volume #1 level 0.08

> volume #1 level 0.3426

> volume #1 level 0.5

> volume #1 level 0.7626

> open
> /Users/irina.grishkovskaya/DRG1/refinement/RealSpaceRefine_107/DRG1_refine_105-coot-1_real_space_refined_107.pdb

Chain information for DRG1_refine_105-coot-1_real_space_refined_107.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
  

> hide atoms

> show cartoons

> select #4

32997 atoms, 33569 bonds, 18 pseudobonds, 4276 residues, 2 models selected  

> ui mousemode right "translate selected models"

> ui mousemode right translate

> hide #!1 models

> hide #!2 models

> hide #!3 models

> show #!1 models

> show #!2 models

> show #!3 models

> select up

32997 atoms, 33569 bonds, 18 pseudobonds, 4276 residues, 2 models selected  

> select up

176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected  

> select up

176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected  

> select up

176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected  

> select up

176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected  

> select up

176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected  

> select up

176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected  

> select up

176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected  

> select up

176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected  

> select up

176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected  

> select up

176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected  

> select up

176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 7 models selected  

> ~select #1

176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 5 models selected  

> ~select #2

176933 atoms, 187894 bonds, 18 pseudobonds, 16321 residues, 3 models selected  

> select #3

143936 atoms, 154325 bonds, 5 pseudobonds, 12045 residues, 2 models selected  

> ~select #3

Nothing selected  

> select #4

32997 atoms, 33569 bonds, 18 pseudobonds, 4276 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,293.9,0,1,0,303.38,0,0,1,237.15

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.99339,-0.031618,-0.11034,314.43,-0.021212,0.89418,-0.44721,382.73,0.1128,0.4466,0.8876,175.02

> view matrix models
> #4,-0.13699,0.61646,-0.77538,474.34,-0.82664,0.36015,0.43238,447.85,0.5458,0.70019,0.46025,138.37

> view matrix models
> #4,-0.53811,0.8022,0.25866,361.91,-0.40768,-0.51631,0.75314,466.5,0.73772,0.29982,0.60487,147.08

> view matrix models
> #4,-0.014725,-0.93197,-0.36223,614.8,-0.97396,-0.068592,0.21607,557.7,-0.22622,0.35598,-0.9067,482.6

> view matrix models
> #4,0.44051,-0.55614,-0.70474,546.4,-0.16551,-0.82187,0.54511,503.72,-0.88236,-0.12348,-0.45409,578.24

> view matrix models
> #4,0.68532,0.12183,-0.71798,420.08,0.66217,-0.51458,0.54473,345.56,-0.30309,-0.84874,-0.43333,594.95

> view matrix models
> #4,0.99514,-0.073317,-0.06579,313.82,0.020067,-0.50299,0.86406,389.58,-0.096442,-0.86118,-0.49907,576.87

> view matrix models
> #4,0.99478,-0.07468,-0.069557,314.57,0.022447,-0.50476,0.86297,389.65,-0.099556,-0.86002,-0.50045,577.34

> view matrix models
> #4,0.88258,-0.20625,-0.42252,397.2,0.2146,-0.62287,0.75232,394.44,-0.41834,-0.75465,-0.50547,607.97

> view matrix models
> #4,0.77877,-0.23223,-0.58274,437.42,0.34826,-0.6126,0.70954,380.25,-0.52176,-0.75551,-0.3962,607.45

> view matrix models
> #4,0.97949,0.19468,-0.051991,276.96,0.1962,-0.98022,0.025863,546.8,-0.045927,-0.035533,-0.99831,524.31

> view matrix models
> #4,0.98426,0.17645,-0.0096685,272.98,0.17671,-0.98279,0.05385,546.02,-3.9982e-07,-0.054711,-0.9985,520.58

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.98426,0.17645,-0.0096685,255.63,0.17671,-0.98279,0.05385,546.06,-3.9982e-07,-0.054711,-0.9985,515.55

> view matrix models
> #4,0.98426,0.17645,-0.0096685,260.55,0.17671,-0.98279,0.05385,547.49,-3.9982e-07,-0.054711,-0.9985,518.03

> view matrix models
> #4,0.99514,0.091382,0.036657,264.42,0.093376,-0.994,-0.056971,575.98,0.031231,0.060117,-0.9977,497.64

> ~select #4

Nothing selected  

> select #4

32997 atoms, 33569 bonds, 18 pseudobonds, 4276 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.95478,0.27638,0.10959,234.36,0.24497,-0.94018,0.23676,506.8,0.16846,-0.19921,-0.96537,509.94

> view matrix models
> #4,0.99171,-0.042032,-0.12142,305.21,-0.056676,-0.99118,-0.11979,605.23,-0.11531,0.12568,-0.98535,507.32

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.99171,-0.042032,-0.12142,304.59,-0.056676,-0.99118,-0.11979,605.01,-0.11531,0.12568,-0.98535,506.66

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.99171,-0.042032,-0.12142,359.47,-0.056676,-0.99118,-0.11979,652.22,-0.11531,0.12568,-0.98535,516.95

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.96814,0.17115,-0.18278,341.69,0.21016,-0.95225,0.22147,562.45,-0.13615,-0.25283,-0.95788,568.52

> view matrix models
> #4,0.89033,-0.44312,-0.10468,426.91,0.23927,0.65094,-0.72044,466.23,0.38738,0.61638,0.68557,148.09

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.89033,-0.44312,-0.10468,362.33,0.23927,0.65094,-0.72044,437.09,0.38738,0.61638,0.68557,152.87

> ui mousemode right translate

> ~select #4

Nothing selected  

> ui tool show "Volume Viewer"

> ui tool show "Fit in Map"

Fit molecule 2108046n8k_widetargetDEv1in-coot-18.pdb (#3) to map
cryosparc_P144_J2263_002_volume_map.mrc (#1) using 143936 atoms  
average map value = 0.325, steps = 68  
shifted from previous position = 1.08  
rotated from previous position = 2.49 degrees  
atoms outside contour = 125881, contour level = 0.76261  
  
Position of 2108046n8k_widetargetDEv1in-coot-18.pdb (#3) relative to
cryosparc_P144_J2263_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99919002 -0.01132363 0.03861454 -8.92170616  
0.01195645 0.99979734 -0.01619664 0.75058976  
-0.03842331 0.01664522 0.99912291 6.60465751  
Axis 0.37783275 0.88629030 0.26782815  
Axis point 173.27376536 0.00000000 225.51392121  
Rotation angle (degrees) 2.49090756  
Shift along axis -0.93675914  
  
Fit molecule 2108046n8k_widetargetDEv1in-coot-18.pdb (#3) to map
cryosparc_P144_J2263_002_volume_map.mrc (#1) using 143936 atoms  
average map value = 0.325, steps = 40  
shifted from previous position = 0.012  
rotated from previous position = 0.00439 degrees  
atoms outside contour = 125874, contour level = 0.76261  
  
Position of 2108046n8k_widetargetDEv1in-coot-18.pdb (#3) relative to
cryosparc_P144_J2263_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99919171 -0.01136655 0.03855810 -8.88665146  
0.01199727 0.99979734 -0.01616587 0.73839814  
-0.03836654 0.01661540 0.99912559 6.59176319  
Axis 0.37757322 0.88601453 0.26910353  
Axis point 173.18551761 0.00000000 225.02471942  
Rotation angle (degrees) 2.48801927  
Shift along axis -0.92726337  
  

> select #4

32997 atoms, 33569 bonds, 18 pseudobonds, 4276 residues, 2 models selected  

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.89033,-0.44312,-0.10468,376.2,0.23927,0.65094,-0.72044,426.44,0.38738,0.61638,0.68557,147.83

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.70858,-0.37826,0.59568,295.93,0.65079,0.023998,-0.75888,461.13,0.27276,0.92539,0.26317,179.33

> view matrix models
> #4,0.96289,-0.22263,0.15255,300,0.22664,0.36015,-0.90495,493.96,0.14653,0.90594,0.39724,181.16

> view matrix models
> #4,0.85579,-0.4859,0.17753,348,0.328,0.24427,-0.91255,496.91,0.40004,0.83919,0.36842,158.97

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.85579,-0.4859,0.17753,348.37,0.328,0.24427,-0.91255,499.36,0.40004,0.83919,0.36842,159.36

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.91478,-0.40278,0.03057,348.89,0.18994,0.36212,-0.91258,502.32,0.3565,0.84062,0.40776,159.81

> ~select #4

Nothing selected  
Fit molecule 2108046n8k_widetargetDEv1in-coot-18.pdb (#3) to map
cryosparc_P144_J2263_002_volume_map.mrc (#1) using 143936 atoms  
average map value = 0.325, steps = 44  
shifted from previous position = 0.00964  
rotated from previous position = 0.00246 degrees  
atoms outside contour = 125871, contour level = 0.76261  
  
Position of 2108046n8k_widetargetDEv1in-coot-18.pdb (#3) relative to
cryosparc_P144_J2263_002_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99919166 -0.01133239 0.03856944 -8.90422619  
0.01196423 0.99979734 -0.01619065 0.76624848  
-0.03837814 0.01663901 0.99912475 6.58637871  
Axis 0.37804109 0.88606903 0.26826594  
Axis point 172.90904166 0.00000000 225.46553009  
Rotation angle (degrees) 2.48860878  
Shift along axis -0.92031319  
  

> save
> /Users/irina.grishkovskaya/DRG1/Bud20/Krios/210812_Buds20_J2263/DRG1_fit_JJ2263_P144.pdb
> models #4 relModel #2

> save
> /Users/irina.grishkovskaya/DRG1/Bud20/Krios/210812_Buds20_J2263/cryosparc_P144_J2263_flip.mrc
> models #2

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/__init__.py", line 164, in save  
save_map(session, path, _name, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 3974, in save_map  
save_grid_data(grids, path, session, format_name, options)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_data/fileformats.py", line 297, in save_grid_data  
if matching_grid_path(glist, path):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_data/fileformats.py", line 340, in matching_grid_path  
if realpath(gp) == rp:  
File
"/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py",
line 392, in realpath  
return abspath(path)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py",
line 379, in abspath  
cwd = os.getcwd()  
FileNotFoundError: [Errno 2] No such file or directory  
  
FileNotFoundError: [Errno 2] No such file or directory  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py",
line 379, in abspath  
cwd = os.getcwd()  
  
See log for complete Python traceback.  
  

>
> /Users/irina.grishkovskaya/DRG1/Bud20/Krios/210812_Buds20_J2263/cryosparc_P144_J2263_flip.mrc
> models #2

Unknown command:
/Users/irina.grishkovskaya/DRG1/Bud20/Krios/210812_Buds20_J2263/cryosparc_P144_J2263_flip.mrc
models #2  

> save
> /Users/irina.grishkovskaya/DRG1/Bud20/Krios/210812_Buds20_J2263/cryosparc_P144_J2263_flip.mrc
> models #2

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/__init__.py", line 164, in save  
save_map(session, path, _name, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 3974, in save_map  
save_grid_data(grids, path, session, format_name, options)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_data/fileformats.py", line 297, in save_grid_data  
if matching_grid_path(glist, path):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_data/fileformats.py", line 340, in matching_grid_path  
if realpath(gp) == rp:  
File
"/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py",
line 392, in realpath  
return abspath(path)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py",
line 379, in abspath  
cwd = os.getcwd()  
FileNotFoundError: [Errno 2] No such file or directory  
  
FileNotFoundError: [Errno 2] No such file or directory  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/posixpath.py",
line 379, in abspath  
cwd = os.getcwd()  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.19
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2,9 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 429.60.3.0.0
      SMC Version (system): 2.45f4

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H114)
      Kernel Version: Darwin 19.6.0
      Time since boot: 17:33

Graphics/Displays:

    Intel HD Graphics 630:

      Chipset Model: Intel HD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x591b
      Revision ID: 0x0004
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro 560:

      Chipset Model: Radeon Pro 560
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c0
      ROM Revision: 113-C980AJ-927
      VBIOS Version: 113-C9801AU-A02
      EFI Driver Version: 01.A0.927
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    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-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-Label: 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
    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
    matplotlib-inline: 0.1.2
    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: 1.3.0

Change History (3)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → os.getcwd() failure saving map

comment:2 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

You denied permission for ChimeraX to access the the Desktop folder. Even though you were not saving files to the desktop the saving code asked for the current working directory which is Desktop for ChimeraX and that failed. The simple solution is to allow ChimeraX to access the Desktop. You can change this setting using Mac system settings / Security & Privacy / Files & Folders / UCSF ChimeraX / Desktop Folder -> enable.

I have improved the code so it does not try to get the current working directory when saving the map. So the daily build will not give this error.

in reply to:  3 ; comment:3 by irina.grishkovskaya@…, 4 years ago 

Dear Tom,
Many thanks for such simple solution 😊. Its solved all the issues also Isolde installed now!
BR,
Irina

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Friday, 13. August 2021 at 02:10
To:
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, Grishkovskaya,Irina <irina.grishkovskaya@imp.ac.at>
Subject: Re: [ChimeraX] #5042: os.getcwd() failure saving map
#5042: os.getcwd() failure saving map
--------------------------------------------+-------------------------
          Reporter:  irina.grishkovskaya@…  |      Owner:  Tom Goddard
              Type:  defect                 |     Status:  closed
          Priority:  normal                 |  Milestone:
         Component:  Input/Output           |    Version:
        Resolution:  fixed                  |   Keywords:
        Blocked By:                         |   Blocking:
Notify when closed:                         |   Platform:  all
           Project:  ChimeraX               |
--------------------------------------------+-------------------------
Changes (by Tom Goddard):

 * status:  assigned => closed
 * resolution:   => fixed


Comment:

 You denied permission for ChimeraX to access the the Desktop folder.  Even
 though you were not saving files to the desktop the saving code asked for
 the current working directory which is Desktop for ChimeraX and that
 failed.  The simple solution is to allow ChimeraX to access the Desktop.
 You can change this setting using Mac system settings / Security & Privacy
 / Files & Folders / UCSF ChimeraX / Desktop Folder -> enable.

 I have improved the code so it does not try to get the current working
 directory when saving the map.  So the daily build will not give this
 error.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5042#comment:2>
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