From harijay at gmail.com Thu Jul 19 17:16:08 2007 From: harijay at gmail.com (hari jayaram) Date: Thu Jul 19 17:16:16 2007 Subject: [Jalview-discuss] Jalview applet and menubar Message-ID: Hi really like using jalview.. I normally use it offline using webstart. Today I tried to launch it as an applet on my mac from the pfam database at http://www.sanger.ac.uk/Software/Pfam/ I am using the Java 1.5.0 plugin. How do I get the applet window to show the menu-bar containing file -edit-search etc options? The only menu bar I see on the mac is my firefox menubar even though the mouse focus is on the applet window. Without the menu bar I am powerless..your help will be greatly appreciated thanks Hari Jayaram Postdoc Brandeis University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.jalview.org/pipermail/jalview-discuss/attachments/20070719/b0a1252b/attachment.htm From jimp at compbio.dundee.ac.uk Tue Jul 24 23:44:00 2007 From: jimp at compbio.dundee.ac.uk (Jim Procter) Date: Tue Jul 24 23:44:13 2007 Subject: [Jalview-discuss] Re: Jalview-discuss post from sebastien.moretti@unil.ch requires approval In-Reply-To: References: Message-ID: <46A680B0.1020908@compbio.dundee.ac.uk> Hi Hari and Sebastien, I'm forwarding your message since I'm outwith the domain for administering the list (and a bit confused, here in vienna at the ISMB/ECCB). You're quite right, the menu bar is errant between different browsers on the Mac, IIRC the menus appear in the drop down bar at the top of the screen with firefox (but I'd have to check this - since you haven't noticed them). Give me a few days to get at a mac again and I'll have a look. cheers. Jim > > From: > Sebastien Moretti > Date: > Tue, 24 Jul 2007 10:48:38 +0200 > To: > jalview-discuss@jalview.org > > To: > jalview-discuss@jalview.org > > > Hi Hari. > > I noticed the same behaviour with Firefox on Mac. > > The JalView menubar seems to be only available with Safari. > >> Hi really like using jalview.. >> I normally use it offline using webstart. Today I tried to launch it >> as an applet on my mac from the pfam database at >> http://www.sanger.ac.uk/Software/Pfam/ >> >> >> I am using the Java 1.5.0 plugin. >> >> How do I get the applet window to show the menu-bar containing file >> -edit-search etc options? >> The only menu bar I see on the mac is my firefox menubar even though >> the mouse focus is on the applet window. >> >> Without the menu bar I am powerless..your help will be greatly >> appreciated >> >> thanks >> Hari Jayaram >> Postdoc >> Brandeis University >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Jalview-discuss mailing list >> Jalview-discuss@jalview.org >> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss > > > > ------------------------------------------------------------------------ > > Subject: > confirm 10949ae8436a06fbd094373accbc047580db8cfa > From: > jalview-discuss-request@jalview.org > > > If you reply to this message, keeping the Subject: header intact, > Mailman will discard the held message. Do this if the message is > spam. If you reply to this message and include an Approved: header > with the list password in it, the message will be approved for posting > to the list. The Approved: header can also appear in the first line > of the body of the reply. > -- ------------------------------------------------------------------- J. B. Procter (VAMSAS Project) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk From jimp at compbio.dundee.ac.uk Wed Jul 25 19:11:53 2007 From: jimp at compbio.dundee.ac.uk (Jim Procter) Date: Wed Jul 25 19:12:11 2007 Subject: [Jalview-discuss] No applet menu bar in Firefox (was Re: Jalview-discuss post from sebastien.moretti@unil.ch requires approval) In-Reply-To: <46A680B0.1020908@compbio.dundee.ac.uk> References: <46A680B0.1020908@compbio.dundee.ac.uk> Message-ID: <46A79269.4000102@compbio.dundee.ac.uk> Further to the Jim Procter wrote: > You're quite right, the menu bar is errant between different browsers > on the Mac, IIRC the menus appear in the drop down bar at the top of > the screen with firefox (but I'd have to check this - since you > haven't noticed them). Give me a few days to get at a mac again and > I'll have a look. I have no mac to hand but I remember the issue now. For some reason, pull down menus on any applet window are tagged on to the *right* of the pulldowns on the Firefox menu bar. This is incredibly useless, and seemed to be something to do with the java plugin rather than firefox itself (since I tried various different mac ports to see if that made a difference). unimpressed. Jim From pcieplak at burnham.org Sat Jul 28 06:04:10 2007 From: pcieplak at burnham.org (Piotr Cieplak) Date: Sat Jul 28 06:04:40 2007 Subject: [Jalview-discuss] problems with linking structure of the modelled protein with sequence Message-ID: <001501c7d0d4$bb9b9bd0$08f0010a@CIEPLAK6851> I ma having problems with linking structure to the sequence in Jalview alignment. I can successfully do that for "real" pdb structures taken from PDB, I cannot do this for proteins structure that is a model build by some modeler tools (for example modeler). Is there any solution for that? Thanks Piotr Cieplak -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.jalview.org/pipermail/jalview-discuss/attachments/20070727/63a55c1c/attachment.htm From jimp at compbio.dundee.ac.uk Mon Jul 30 14:11:20 2007 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Mon Jul 30 14:11:34 2007 Subject: [Jalview-discuss] problems with linking structure of the modelled protein with sequence In-Reply-To: <001501c7d0d4$bb9b9bd0$08f0010a@CIEPLAK6851> References: <001501c7d0d4$bb9b9bd0$08f0010a@CIEPLAK6851> Message-ID: <46ADE378.5060700@compbio.dundee.ac.uk> Hi Piotr. A small bugfix is going into the next release which fixes this. Jalview's PDB parser relied on finding a meaningful PDB ID from the TITLE entry in the file, and Modeller doesn't write this in. I only discovered this myself after a half hour of frustration after building some models. A quick work around is to add in a Piotr Cieplak wrote: > I ma having problems with linking structure to the sequence in Jalview > alignment. I can successfully do that for "real" pdb structures taken > from PDB, I cannot do this for proteins structure that is a model build > by some modeler tools (for example modeler). > > Is there any solution for that? > Thanks > Piotr Cieplak From jimp at compbio.dundee.ac.uk Mon Jul 30 15:51:47 2007 From: jimp at compbio.dundee.ac.uk (Jim Procter) Date: Mon Jul 30 15:53:04 2007 Subject: [Jalview-discuss] problems with linking structure of the modelled protein with sequence (workaround) In-Reply-To: <46ADE378.5060700@compbio.dundee.ac.uk> References: <001501c7d0d4$bb9b9bd0$08f0010a@CIEPLAK6851> <46ADE378.5060700@compbio.dundee.ac.uk> Message-ID: <46ADFB03.1010504@compbio.dundee.ac.uk> Oops. I forgot to finish this email. James Procter wrote: > A quick work around is to add in a .. dummy line in the PDB file that you are trying to read in: HEADER 9mdlXX This will ensure the (broken) parser puts in a valid string into the PDB ID variable, and so avoiding the exception that leads to Jalview thinking it cannot read this file as a PDB file. cheers. Jim -- ------------------------------------------------------------------- J. B. Procter (VAMSAS Project) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk From pcieplak at burnham.org Tue Jul 31 17:25:30 2007 From: pcieplak at burnham.org (Piotr Cieplak) Date: Tue Jul 31 17:26:09 2007 Subject: [Jalview-discuss] how to group and display several residues at once Message-ID: <000001c7d38f$69a39220$ccfc10ac@CIEPLAK6851> 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? I can only find a way to display single specific residue that is selected by hoovering mouse over it in the sequence display. Thanks Piotr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.jalview.org/pipermail/jalview-discuss/attachments/20070731/dcaa587b/attachment.htm