Hello,
I am trying to associate a pdb structure with a sequence, following the procedure as outline in the help/documentation:
"Associating PDB files with Sequences
To associate PDB files with a sequence, right click on a sequence ID and select "Structure→ Associate Structure with Sequence", and one of the submenus:
From File - You can load a PDB file from the local machine or network and associate it with the selected sequence. PDB files associated in this way will also be saved in the Jalview Archive file."
However, when I select 'From File' nothing happens. I would have expected a file selection dialogue box. In the Java Console, the following messages appear:
Exception in thread "AWT-EventQueue-0" java.lang.NumberFormatException: For input string: "pdbRefSeq"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:492)
at java.lang.Integer.<init>(Integer.java:677)
at jalview.gui.PopupMenu.pdbFromFile_actionPerformed(PopupMenu.java:1955)
at jalview.gui.PopupMenu$30.actionPerformed(PopupMenu.java:1061)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
at java.awt.Component.processMouseEvent(Component.java:6505)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3321)
at java.awt.Component.processEvent(Component.java:6270)
at java.awt.Container.processEvent(Container.java:2229)
at java.awt.Component.dispatchEventImpl(Component.java:4861)
at java.awt.Container.dispatchEventImpl(Container.java:2287)
at java.awt.Component.dispatchEvent(Component.java:4687)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
at java.awt.Container.dispatchEventImpl(Container.java:2273)
at java.awt.Window.dispatchEventImpl(Window.java:2719)
at java.awt.Component.dispatchEvent(Component.java:4687)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:723)
at java.awt.EventQueue.access$200(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:682)
at java.awt.EventQueue$3.run(EventQueue.java:680)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
at java.awt.EventQueue$4.run(EventQueue.java:696)
at java.awt.EventQueue$4.run(EventQueue.java:694)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:693)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
I am using the following system:
Jalview Desktop 2.8.1
Build Date: 04 June 2014
Java version: 1.7.0_10
x86 Windows 7 6.1
Many thanks
Andreas
ah - that's most definitely a bug... but we've already patched it
(http://issues.jalview.org/browse/JAL-1530)
If you'd care to save your current project, switch to the latest 2.8.1
build available at the bottom of this page:
http://www.jalview.org/development/development-builds
and then load up your sequences again then the dialog should work!
Happy Jalviewing
Jim.
···
On 08/10/2014 16:33, Kukol, Andreas wrote:
Hello,
I am trying to associate a pdb structure with a sequence, following the procedure as outline in the help/documentation:
"Associating PDB files with Sequences
To associate PDB files with a sequence, right click on a sequence ID and select "Structure→ Associate Structure with Sequence", and one of the submenus:
>From File - You can load a PDB file from the local machine or network and associate it with the selected sequence. PDB files associated in this way will also be saved in the Jalview Archive file."
However, when I select 'From File' nothing happens. I would have expected a file selection dialogue box. In the Java Console, the following messages appear:
Exception in thread "AWT-EventQueue-0" java.lang.NumberFormatException: For input string: "pdbRefSeq"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:492)
at java.lang.Integer.<init>(Integer.java:677)
at jalview.gui.PopupMenu.pdbFromFile_actionPerformed(PopupMenu.java:1955)
at jalview.gui.PopupMenu$30.actionPerformed(PopupMenu.java:1061)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
at java.awt.Component.processMouseEvent(Component.java:6505)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3321)
at java.awt.Component.processEvent(Component.java:6270)
at java.awt.Container.processEvent(Container.java:2229)
at java.awt.Component.dispatchEventImpl(Component.java:4861)
at java.awt.Container.dispatchEventImpl(Container.java:2287)
at java.awt.Component.dispatchEvent(Component.java:4687)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
at java.awt.Container.dispatchEventImpl(Container.java:2273)
at java.awt.Window.dispatchEventImpl(Window.java:2719)
at java.awt.Component.dispatchEvent(Component.java:4687)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:723)
at java.awt.EventQueue.access$200(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:682)
at java.awt.EventQueue$3.run(EventQueue.java:680)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
at java.awt.EventQueue$4.run(EventQueue.java:696)
at java.awt.EventQueue$4.run(EventQueue.java:694)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:693)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
I am using the following system:
Jalview Desktop 2.8.1
Build Date: 04 June 2014
Java version: 1.7.0_10
x86 Windows 7 6.1
Many thanks
Andreas
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