Details
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Type: Bug
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Status: Open
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Priority: Blocker
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Resolution: Unresolved
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Affects Version/s: 2.11.2.7, 2.11.3.0
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Fix Version/s: 2.12.0
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Component/s: jvdesktop, Structures
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Labels:
Description
This affect 2.8 onwards (and probably earlier).
1. On a Windows 7 PC with a samba-mounted home directory, drag a local PDB file from the home directory to the Jalview desktop.
2. Right click the sequence(s) and try to view the structure via the 'cached PDB' view.
Jmol reports it couldn't load the file. Console dump below.
Jalview Version: Development Branch Build
Jalview Installation: webstart git-commit:f37ae4b [develop]
Build Date: 17 October 2016
Java version: 1.8.0_65
amd64 Windows 7 6.1
(C) 2012 Jmol Development
Jmol Version: 14.2.14_2015.06.01 2015-06-01 19:39
java.vendor: Java: Oracle Corporation
java.version: Java 1.8.0_65
os.name: Windows 7
Access: ALL
memory: 55.8/469.8
processors available: 8
useCommandThread: false
FileManager.getAtomSetCollectionFromFile(\\\\gjb-smb.lifesci.dundee.ac.uk\\jprocter\\Downloads\\c2olpB_.5.pdb)
cacheGet file:///gjb-smb.lifesci.dundee.ac.uk/jprocter/Downloads/gjb-smb.lifesci.dundee.ac.uk/jprocter/Downloads/c2olpB_.5.pdb false
cacheGet file:///gjb-smb.lifesci.dundee.ac.uk/jprocter/Downloads/gjb-smb.lifesci.dundee.ac.uk/jprocter/Downloads/c2olpB_.5.pdb false
FileManager opening 2 \\gjb-smb.lifesci.dundee.ac.uk\jprocter\Downloads\gjb-smb.lifesci.dundee.ac.uk\jprocter\Downloads\c2olpB_.5.pdb
Time for openFile(\\\\gjb-smb.lifesci.dundee.ac.uk\\jprocter\\Downloads\\c2olpB_.5.pdb): 57 ms
file ERROR: \\gjb-smb.lifesci.dundee.ac.uk\jprocter\Downloads\gjb-smb.lifesci.dundee.ac.uk\jprocter\Downloads\c2olpB_.5.pdb
java.io.FileNotFoundException: \\gjb-smb.lifesci.dundee.ac.uk\jprocter\Downloads\gjb-smb.lifesci.dundee.ac.uk\jprocter\Downloads\c2olpB_.5.pdb (The system cannot find the path specified)
eval ERROR: Eval
pc:0
1 statements
----
Token[keyword(3/0x8101403) value="load"]
Token[keyword(7/0x49501207) value="file"]
Token[string(4/0x4) value="\\\\gjb-smb.lifesci.dundee.ac.uk\\jprocter\\Downloads\\c2olpB_.5.pdb"]
END
Timed out waiting for Jmol to load files after 20020ms
1. On a Windows 7 PC with a samba-mounted home directory, drag a local PDB file from the home directory to the Jalview desktop.
2. Right click the sequence(s) and try to view the structure via the 'cached PDB' view.
Jmol reports it couldn't load the file. Console dump below.
Jalview Version: Development Branch Build
Jalview Installation: webstart git-commit:f37ae4b [develop]
Build Date: 17 October 2016
Java version: 1.8.0_65
amd64 Windows 7 6.1
(C) 2012 Jmol Development
Jmol Version: 14.2.14_2015.06.01 2015-06-01 19:39
java.vendor: Java: Oracle Corporation
java.version: Java 1.8.0_65
os.name: Windows 7
Access: ALL
memory: 55.8/469.8
processors available: 8
useCommandThread: false
FileManager.getAtomSetCollectionFromFile(\\\\gjb-smb.lifesci.dundee.ac.uk\\jprocter\\Downloads\\c2olpB_.5.pdb)
cacheGet file:///gjb-smb.lifesci.dundee.ac.uk/jprocter/Downloads/gjb-smb.lifesci.dundee.ac.uk/jprocter/Downloads/c2olpB_.5.pdb false
cacheGet file:///gjb-smb.lifesci.dundee.ac.uk/jprocter/Downloads/gjb-smb.lifesci.dundee.ac.uk/jprocter/Downloads/c2olpB_.5.pdb false
FileManager opening 2 \\gjb-smb.lifesci.dundee.ac.uk\jprocter\Downloads\gjb-smb.lifesci.dundee.ac.uk\jprocter\Downloads\c2olpB_.5.pdb
Time for openFile(\\\\gjb-smb.lifesci.dundee.ac.uk\\jprocter\\Downloads\\c2olpB_.5.pdb): 57 ms
file ERROR: \\gjb-smb.lifesci.dundee.ac.uk\jprocter\Downloads\gjb-smb.lifesci.dundee.ac.uk\jprocter\Downloads\c2olpB_.5.pdb
java.io.FileNotFoundException: \\gjb-smb.lifesci.dundee.ac.uk\jprocter\Downloads\gjb-smb.lifesci.dundee.ac.uk\jprocter\Downloads\c2olpB_.5.pdb (The system cannot find the path specified)
eval ERROR: Eval
pc:0
1 statements
----
Token[keyword(3/0x8101403) value="load"]
Token[keyword(7/0x49501207) value="file"]
Token[string(4/0x4) value="\\\\gjb-smb.lifesci.dundee.ac.uk\\jprocter\\Downloads\\c2olpB_.5.pdb"]
END
Timed out waiting for Jmol to load files after 20020ms
Attachments
Issue Links
- related with
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JAL-2465 No mapping generated for 3D Structures loaded in Jmol via URL
- Closed