Opened 4 years ago

Closed 4 years ago

#4831 closed defect (nonchimerax)

Opening MRC file: getcwd: No such file or directory

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
(Describe the actions that caused this problem to occur here)
save mrc file

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/DRG1/Bud20/Krios/J2114/6n8k_JJ2114v2.pdb
> format pdb

No such file/path:
/Users/irina.grishkovskaya/DRG1/Bud20/Krios/J2114/6n8k_JJ2114v2.pdb  

> ui tool show "Command Line Interface"

> ui tool show "Model Panel"

> open "/Users/irina.grishkovskaya/Dropbox
> (VBC)/Bergler_lab/Drg1_Manuscripts/Maps and
> Models/models/RealSpaceRefine_67/DRGall_v7inputfin_cart_relax_0001_real_space_refined_067.pdb"
> format pdb

Chain information for
DRGall_v7inputfin_cart_relax_0001_real_space_refined_067.pdb #1  
---  
Chain | Description  
A | No description available  
B C E | No description available  
D | No description available  
F | No description available  
G | No description available  
  

> close

> open
> /Users/irina.grishkovskaya/DRG1/Bud20/Krios/deepEMhancer_results/wideTarget_cryosparc_P144_J2114_003_volume_map_flip.mrc
> format mrc

Opened wideTarget_cryosparc_P144_J2114_003_volume_map_flip.mrc as #1, grid
size 480,480,480, pixel 1.38, shown at level 0.00126, step 2, values float32  

> close

> open
> /Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/deepEMhancer_results/highRes_run_class001.mrc

Opened highRes_run_class001.mrc as #1, grid size 480,480,480, pixel 1.38,
shown at level 0.0292, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.1647

> close

> open
> /Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/deepEMhancer_results/tightTarget_run_class001.mrc

Opened tightTarget_run_class001.mrc as #1, grid size 480,480,480, pixel 1.38,
shown at level 0.000417, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.1759

> open
> /Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/deepEMhancer_results/wideTarget_run_class001.mrc

Opened wideTarget_run_class001.mrc as #2, grid size 480,480,480, pixel 1.38,
shown at level 0.0031, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.03636

> volume #2 level -0.005259

> volume #2 level 0.02467

> volume flip #2 axis z

Opened wideTarget_run_class001.mrc z flip as #3, grid size 480,480,480, pixel
1.38, shown at step 1, values float32  

> open
> /Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/210625_relion_all

'/Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/210625_relion_all'
has no suffix  

> open
> /Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/210625_relion_all.pdb

Chain information for 210625_relion_all.pdb #4  
---  
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  
M2 | 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  
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 #3.1 50

> set bgColor white

> close #1

> close #2

> ui tool show "Fit in Map"

Fit molecule 210625_relion_all.pdb (#4) to map wideTarget_run_class001.mrc z
flip (#3) using 140596 atoms  
average map value = 0.3387, steps = 44  
shifted from previous position = 0.0242  
rotated from previous position = 0.0131 degrees  
atoms outside contour = 18373, contour level = 0.024672  
  
Position of 210625_relion_all.pdb (#4) relative to wideTarget_run_class001.mrc
z flip (#3) coordinates:  
Matrix rotation and translation  
0.99999997 -0.00009087 -0.00020933 0.10595249  
0.00009086 1.00000000 -0.00002058 -0.00249061  
0.00020933 0.00002056 0.99999998 -0.06642199  
Axis 0.08976002 -0.91360588 0.39656959  
Axis point 289.78061388 0.00000000 512.34849578  
Rotation angle (degrees) 0.01312814  
Shift along axis -0.01455521  
  
Fit molecule 210625_relion_all.pdb (#4) to map wideTarget_run_class001.mrc z
flip (#3) using 140596 atoms  
average map value = 0.3387, steps = 40  
shifted from previous position = 0.00152  
rotated from previous position = 0.00102 degrees  
atoms outside contour = 18373, contour level = 0.024672  
  
Position of 210625_relion_all.pdb (#4) relative to wideTarget_run_class001.mrc
z flip (#3) coordinates:  
Matrix rotation and translation  
0.99999998 -0.00007413 -0.00020980 0.10075919  
0.00007413 1.00000000 -0.00002645 0.00641076  
0.00020980 0.00002643 0.99999998 -0.06813662  
Axis 0.11799236 -0.93628879 0.33081883  
Axis point 298.55929612 0.00000000 489.59701403  
Rotation angle (degrees) 0.01283861  
Shift along axis -0.01665438  
  
Fit molecule 210625_relion_all.pdb (#4) to map wideTarget_run_class001.mrc z
flip (#3) using 140596 atoms  
average map value = 0.3388, steps = 28  
shifted from previous position = 0.0233  
rotated from previous position = 7.14e-05 degrees  
atoms outside contour = 18392, contour level = 0.024672  
  
Position of 210625_relion_all.pdb (#4) relative to wideTarget_run_class001.mrc
z flip (#3) coordinates:  
Matrix rotation and translation  
0.99999998 -0.00007426 -0.00020937 0.09901143  
0.00007426 1.00000000 -0.00002761 -0.01550909  
0.00020937 0.00002759 0.99999998 -0.07494362  
Axis 0.12329870 -0.93528485 0.33172229  
Axis point 360.92998101 0.00000000 471.76702831  
Rotation angle (degrees) 0.01282615  
Shift along axis 0.00185293  
  

> save
> /Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/deepEMhancer_results/2114relion_widetarget_flip.mrc
> models #3

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.  
  

> save
> /Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/deepEMhancer_results/2114relion_wideTarget_run_class001flip.mrc
> models #3

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.  
  

> save
> /Users/irina.grishkovskaya/DRG1/Bud20/Krios/relion_2114/relion2114_wideTarget_run_class001flip.mrc
> models #3

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.  
  

Window position QRect(1967,731 100x30) outside any known screen, using primary
screen  




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: 16 days 2:30

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 (2)

comment:1 by pett, 4 years ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Opening MRC file: getcwd: No such file or directory

comment:2 by Tom Goddard, 4 years ago

Resolution: → nonchimerax
Status: assigned → closed

This error saving an MRC file is because ChimeraX is running in a deleted directory. That should not cause an error, but Python is behaving badly. ChimeraX is calling "realpath(path)" when it is trying to check if you are overwriting a map file with itself (e.g. to change grid spacing), in which case it uses a temporary file. An realpath() is throwing an error because it uses Python getcwd() (get current working directory) and the current directory of ChimeraX has been deleted.

I don't have an easy way to fix this. Python realpath() should not need the current working directory unless the path it is given is a relative path, but apparently it calls it in all cases. I could put in a check for this, but I have seen this getcwd() error in many places in the ChimeraX code and it would be difficult to check every call where Python internally uses getcwd().

So the main fix is not to run ChimeraX in a directory and then delete that directory. I am not sure how you did that unless you ran ChimeraX from a terminal. If you run it by clicking the ChimeraX icon it starts in ~/Desktop and I doubt you deleted the Desktop directory.

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