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#5263 feedback defect

Cannot save PDB

Reported by:	Daniel.haeussler@…	Owned by:	Eric Pettersen
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:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

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 "C:\\\Users\\\AG Krüger\\\Desktop\\\Daniele\\\APP Modellig\\\Published
> Structures\\\6yhf.pdb"

6yhf.pdb title:  
Solution NMR structure of app TMD [more info...]  
  
Chain information for 6yhf.pdb  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | amyloid-β precursor
protein  
  

> set bgColor white

Alignment identifier is 1  
Alignment identifier is 2  

> rainbow

> rainbow

> color byhetero

> mlp

Map values for surface "6yhf.pdb_A SES surface": minimum -23.51, mean 1.959,
maximum 21.85  
Map values for surface "6yhf.pdb_A SES surface": minimum -23.95, mean 1.756,
maximum 21.51  
Map values for surface "6yhf.pdb_A SES surface": minimum -24.35, mean 1.78,
maximum 22.29  
Map values for surface "6yhf.pdb_A SES surface": minimum -23.56, mean 1.721,
maximum 21.97  
Map values for surface "6yhf.pdb_A SES surface": minimum -24.76, mean 1.782,
maximum 22.63  
Map values for surface "6yhf.pdb_A SES surface": minimum -28.08, mean 1.556,
maximum 22.6  
Map values for surface "6yhf.pdb_A SES surface": minimum -25.33, mean 1.745,
maximum 22.18  
Map values for surface "6yhf.pdb_A SES surface": minimum -22.96, mean 1.489,
maximum 22.94  
Map values for surface "6yhf.pdb_A SES surface": minimum -24.28, mean 1.669,
maximum 22.88  
Map values for surface "6yhf.pdb_A SES surface": minimum -24.84, mean 1.944,
maximum 22.3  
Map values for surface "6yhf.pdb_A SES surface": minimum -25.03, mean 1.808,
maximum 21.71  
Map values for surface "6yhf.pdb_A SES surface": minimum -22.37, mean 1.637,
maximum 22.12  
Map values for surface "6yhf.pdb_A SES surface": minimum -25.09, mean 1.399,
maximum 21.54  
Map values for surface "6yhf.pdb_A SES surface": minimum -23.05, mean 1.732,
maximum 21.54  
Map values for surface "6yhf.pdb_A SES surface": minimum -24.16, mean 1.676,
maximum 21.52  
Map values for surface "6yhf.pdb_A SES surface": minimum -22.66, mean 1.986,
maximum 22.04  
Map values for surface "6yhf.pdb_A SES surface": minimum -23.04, mean 1.76,
maximum 22.12  
Map values for surface "6yhf.pdb_A SES surface": minimum -22.53, mean 1.731,
maximum 21.66  
Map values for surface "6yhf.pdb_A SES surface": minimum -24.19, mean 1.755,
maximum 21.31  
Map values for surface "6yhf.pdb_A SES surface": minimum -23.29, mean 1.673,
maximum 22.08  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 6yhf.pdb_A SES surface #1.1.1: minimum, -8.90, mean 2.99,
maximum 16.63  
Coulombic values for 6yhf.pdb_A SES surface #1.2.1: minimum, -8.54, mean 2.88,
maximum 16.69  
Coulombic values for 6yhf.pdb_A SES surface #1.3.1: minimum, -9.39, mean 2.70,
maximum 16.93  
Coulombic values for 6yhf.pdb_A SES surface #1.4.1: minimum, -9.59, mean 2.74,
maximum 15.35  
Coulombic values for 6yhf.pdb_A SES surface #1.5.1: minimum, -6.39, mean 2.61,
maximum 13.60  
Coulombic values for 6yhf.pdb_A SES surface #1.6.1: minimum, -7.62, mean 2.82,
maximum 14.28  
Coulombic values for 6yhf.pdb_A SES surface #1.7.1: minimum, -10.12, mean
3.14, maximum 16.87  
Coulombic values for 6yhf.pdb_A SES surface #1.8.1: minimum, -8.27, mean 2.83,
maximum 17.39  
Coulombic values for 6yhf.pdb_A SES surface #1.9.1: minimum, -9.21, mean 3.07,
maximum 16.06  
Coulombic values for 6yhf.pdb_A SES surface #1.10.1: minimum, -9.38, mean
2.87, maximum 16.94  
Coulombic values for 6yhf.pdb_A SES surface #1.11.1: minimum, -8.89, mean
2.93, maximum 19.35  
Coulombic values for 6yhf.pdb_A SES surface #1.12.1: minimum, -9.86, mean
2.95, maximum 16.09  
Coulombic values for 6yhf.pdb_A SES surface #1.13.1: minimum, -10.27, mean
3.06, maximum 16.37  
Coulombic values for 6yhf.pdb_A SES surface #1.14.1: minimum, -10.44, mean
2.79, maximum 18.21  
Coulombic values for 6yhf.pdb_A SES surface #1.15.1: minimum, -8.90, mean
2.88, maximum 16.80  
Coulombic values for 6yhf.pdb_A SES surface #1.16.1: minimum, -10.01, mean
2.78, maximum 15.62  
Coulombic values for 6yhf.pdb_A SES surface #1.17.1: minimum, -10.06, mean
2.96, maximum 15.55  
Coulombic values for 6yhf.pdb_A SES surface #1.18.1: minimum, -9.13, mean
2.69, maximum 17.88  
Coulombic values for 6yhf.pdb_A SES surface #1.19.1: minimum, -9.47, mean
2.85, maximum 16.29  
Coulombic values for 6yhf.pdb_A SES surface #1.20.1: minimum, -8.48, mean
2.90, maximum 16.26  
To also show corresponding color key, enter the above coulombic command and
add key true  

> lighting shadows true

> lighting shadows false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting full

> lighting soft

> lighting full

> lighting flat

> lighting flat

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> lighting soft

> lighting simple

> set bgColor white

> set bgColor gray

> set bgColor black

> set bgColor white

> ui tool show "Side View"

> view

> view

> view orient

> transparency 50

> volume showOutlineBox true

No volumes specified  

> transparency 0

> transparency 50

> volume style image

No volumes specified  

> transparency 0

> volume style mesh

No volumes specified  

> volume style mesh

No volumes specified  

> transparency 50

> volume style image

No volumes specified  

> volume style mesh

No volumes specified  

> volume style surface

No volumes specified  

> volume hide

No volumes specified  

> volume planes z style image imageMode "full region"

No volumes specified  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 20 atomic
models, 0 maps.  

> volume showOutlineBox true

No volumes specified  

> volume appearance airways

No volumes specified  

> volume appearance airways

No volumes specified  

> volume appearance chest

No volumes specified  

> volume appearance brain

No volumes specified  

> volume appearance initial

No volumes specified  

> toolshed show

Downloading bundle ChimeraX_AddH-2.1.3-py3-none-any.whl  
Successfully installed ChimeraX-AddH-2.1.3  
Installed ChimeraX-AddH (2.1.3)  
Downloading bundle SEQCROW-1.2.2-py3-none-any.whl  
Successfully installed SEQCROW-1.2.2 Send2Trash-1.8.0  
Installed SEQCROW (1.2.2)  
Downloading bundle MolecularDynamicsViewer-1.2-py3-none-any.whl  
Successfully installed MolecularDynamicsViewer-1.2  
Installed MolecularDynamicsViewer (1.2)  
Downloading bundle ChimeraX_PDBImages-1.1-py3-none-any.whl  
Bundle saved as C:/Users/AG Krüger/Downloads/ChimeraX_PDBImages-1.1-py3-none-
any.whl  
Downloading bundle ChimeraX_DevelExtras-0.4.0-py3-none-any.whl  
Successfully installed ChimeraX-DevelExtras-0.4.0  
Installed ChimeraX-DevelExtras (0.4.0)  
Downloading bundle ChimeraX_Maestro-1.8.1-py3-none-any.whl  
Successfully installed ChimeraX-Maestro-1.8.1  
Installed ChimeraX-Maestro (1.8.1)  
Replacing data format 'Schrodinger Maestro' as defined by ChimeraX-Maestro
with definition from ChimeraX-Maestro  

> ui mousemode right "crop volume"

> ui mousemode right "contour level"

> ui mousemode right minimize

> ui tool show Contacts

> select #1.1/A

474 atoms, 473 bonds, 30 residues, 1 model selected  

> select ~sel

9006 atoms, 8987 bonds, 570 residues, 20 models selected  

> delete atoms (#!1.2-20 & sel)

> delete bonds (#!1.2-20 & sel)

> surface hidePatches

> cartoon style xsection oval modeHelix default

> cartoon style coil xsection oval

> cartoon style xsection barbell modeHelix default

> save "C:/Users/AG Krüger/Desktop/Daniele/APP Modellig/Published
> Structures/6yhf_.pdb" relModel #1.1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 162, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 379, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1285, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider  
what(session)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\\__init__.py", line 73, in save  
pdb.save_pdb(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb  
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,  
OSError: Unable to open file 'C:/Users/AG Krüger/Desktop/Daniele/APP
Modellig/Published Structures/6yhf_.pdb' for writing  
  
OSError: Unable to open file 'C:/Users/AG Krüger/Desktop/Daniele/APP
Modellig/Published Structures/6yhf_.pdb' for writing  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb  
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,  
  
See log for complete Python traceback.  
  

> save "C:/Users/AG Krüger/Desktop/Daniele/APP Modellig/Published
> Structures/6yhf_.pdb" relModel #1.1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\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 "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\\__init__.py", line 73, in save  
pdb.save_pdb(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb  
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,  
OSError: Unable to open file 'C:/Users/AG Krüger/Desktop/Daniele/APP
Modellig/Published Structures/6yhf_.pdb' for writing  
  
OSError: Unable to open file 'C:/Users/AG Krüger/Desktop/Daniele/APP
Modellig/Published Structures/6yhf_.pdb' for writing  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\pdb\pdb.py", line 193, in save_pdb  
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 457.51
OpenGL renderer: GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Gigabyte Technology Co., Ltd.
Model: X570 AORUS MASTER
OS: Microsoft Windows 10 Education (Build 19043)
Memory: 137,381,068,800
MaxProcessMemory: 137,438,953,344
CPU: 24 AMD Ryzen 9 3900X 12-Core Processor            
OSLanguage: de-DE
Locale: ('de_DE', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    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: 2.1.3
    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-DevelExtras: 0.4.0
    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
    MolecularDynamicsViewer: 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
    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
    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
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    Send2Trash: 1.8.0
    SEQCROW: 1.2.2
    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
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component:	Unassigned → Input/Output
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Reporter:	changed from Danel.haeussler@… to Daniel.haeussler@…
Status:	new → accepted
Summary:	ChimeraX bug report submission → Cannot save PDB

comment:2 by Eric Pettersen, 4 years ago

Status:	accepted → feedback

Hi Daniel,

Thanks for reporting this problem. Are you unable to save PDB files to any folder, or just this particular folder?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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