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 > > _______________________________________________ > Jalview-discuss mailing list > [email protected] > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss _______________________________________________ Jalview-discuss mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
