From jimp at compbio.dundee.ac.uk Wed Aug 1 15:06:07 2007 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Wed Aug 1 15:06:22 2007 Subject: [Jalview-discuss] how to group and display several residues at once In-Reply-To: <000001c7d38f$69a39220$ccfc10ac@CIEPLAK6851> References: <000001c7d38f$69a39220$ccfc10ac@CIEPLAK6851> Message-ID: <46B0934F.5040804@compbio.dundee.ac.uk> Piotr Cieplak wrote: > Hi > Is it any way to select and group together several residues from the > sequence alignment window > and display them in the structure at the PDB viewer? Unfortunately not. You could create a coloured group or a sequence feature on the sequence, so the corresponding structural residues are coloured in the same way. Otherwise, only sequence colours and single residue mouseover highlight positions are sent to the viewer. We realised this was a limitation but have not had the resources to add in any other kind of interaction. > I can only find a way to display single specific residue that is > selected by hoovering mouse > over it in the sequence display. If you are using the application with Jmol then you could also open the Jmol console window and type commands to explicitly display the residue sidechains or use the Jmol menu to set their display style (after adding each residue to the Jmol selection individually). Jim From jimp at compbio.dundee.ac.uk Wed Aug 1 16:28:30 2007 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Wed Aug 1 16:28:38 2007 Subject: [Jalview-discuss] Jalview applet and menubar In-Reply-To: References: Message-ID: <46B0A69E.108@compbio.dundee.ac.uk> Hi all. I've checked on the local minimac, and the story about the jalview applet menu bar and OSX is as follows: Firefox and derivatives running on OSX run java applets as subsidiary application contexts to themselves. This means that as far as OSX is concerned, the user sees the sum of all the current application contexts relevant to the current input focus. Practically, the situation is shown here: http://preview.tinyurl.com/27lan7 The image shows the File menu for the Jalview applet pulled down from the top menu bar, and the Camino pull down menus to the left of it. But, here is the snag - it is impossible to see or get to the File menu for the applet unless you first click in the jalview applet alignment window to give it the input focus (the same is true with the File menu of the jalview applet tree viewer window, or PDB viewer!). If anyone knows any way around this 'feature' of OSX, answers on a postcard to the usual address! ho hum. Jim.