Details
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Type:
Bug
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Status: Open
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Priority:
Critical
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Resolution: Unresolved
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Affects Version/s: 2.11.2.2
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Fix Version/s: 2.11.3
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Component/s: Structures
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Labels:
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Environment:Jalview Version: 2.11.2.2
Jalview Installation: Source git-commit:62fb9a3042 [releases/Release_2_11_2_Branch]
Build Date: 15:43:43 19 April 2022
Java version: 1.8.0_322
x86_64 Mac OS X 10.16
Install4j version: 9.0.5
Install4j template version: 2.11.2.0_F188884b4_C2040e7e728
Launcher version: 1.8.3-1.2.12_JVL
LookAndFeel: Quaqua Leopard FileChooser-only LAF (ch.randelshofer.quaqua.subset.QuaquaLeopardFileChooserLAF)
Getdown appdir: /Applications/Jalview.app/Contents/Resources/app
Java home: /Applications/Jalview.app/Contents/Resources/app/jre/Contents/HomeJalview Version: 2.11.2.2 Jalview Installation: Source git-commit:62fb9a3042 [releases/Release_2_11_2_Branch] Build Date: 15:43:43 19 April 2022 Java version: 1.8.0_322 x86_64 Mac OS X 10.16 Install4j version: 9.0.5 Install4j template version: 2.11.2.0_F188884b4_C2040e7e728 Launcher version: 1.8.3-1.2.12_JVL LookAndFeel: Quaqua Leopard FileChooser-only LAF (ch.randelshofer.quaqua.subset.QuaquaLeopardFileChooserLAF) Getdown appdir: /Applications/Jalview.app/Contents/Resources/app Java home: /Applications/Jalview.app/Contents/Resources/app/jre/Contents/Home
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Urgency:Urgent
Description
Steps to replicate:
Open a release version of Jalview (e.g. 2.11.2.2) and find FER1_SPIOL in the example_2_7.jar.
Right click on the label to choose "3D Structure Data..." and try and open the cached structure file (this is default behaviour) in ChimeraX (have structure viewer preconfigured, or PyMol).
The structure viewer opens but does not open the structure. In ChimeraX's case no error is displayed.
I am 99% certain that this is because the cached file (saved in /var/...) has a ".txt" extension and not (something like) ".cif" or ".pdb".
Fetching the same structure file anew works because this gets cached with a ".cif" file extension.
Steps to fix -- I'm not certain if the .txt filename caching happens because of the project file or newer version of Jalview caching, a mixture of both (or if newer versions of ChimeraX don't work out the content of .txt), but changing the behaviour to cache the file with a .cif or .pdb extension should fix this problem.
Open a release version of Jalview (e.g. 2.11.2.2) and find FER1_SPIOL in the example_2_7.jar.
Right click on the label to choose "3D Structure Data..." and try and open the cached structure file (this is default behaviour) in ChimeraX (have structure viewer preconfigured, or PyMol).
The structure viewer opens but does not open the structure. In ChimeraX's case no error is displayed.
I am 99% certain that this is because the cached file (saved in /var/...) has a ".txt" extension and not (something like) ".cif" or ".pdb".
Fetching the same structure file anew works because this gets cached with a ".cif" file extension.
Steps to fix -- I'm not certain if the .txt filename caching happens because of the project file or newer version of Jalview caching, a mixture of both (or if newer versions of ChimeraX don't work out the content of .txt), but changing the behaviour to cache the file with a .cif or .pdb extension should fix this problem.