Details
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Type: Bug
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Status: Being documented
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Priority: Blocker
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Resolution: Unresolved
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Affects Version/s: 2.11.4.0, 2.11.4.1
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Component/s: Dev and Dep, jvdesktop, Structures
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Labels:
Description
Update for 2.11.4.0 / 2.11.4.1
On a windows machine with a network mount, start jalview, retrieve a uniprot sequence, and then view a structure for it from the PDB (or 3d-beacons). Save the project.
Now try to load the project - import fails with the same 'file not found' error thrown by Jmol.
----
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
On a windows machine with a network mount, start jalview, retrieve a uniprot sequence, and then view a structure for it from the PDB (or 3d-beacons). Save the project.
Now try to load the project - import fails with the same 'file not found' error thrown by Jmol.
----
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