From william at cryst.bioc.cam.ac.uk Thu Jul 2 16:19:31 2009 From: william at cryst.bioc.cam.ac.uk (William Ross Pitt) Date: Thu, 02 Jul 2009 16:19:31 +0100 Subject: [Jalview-discuss] Protein structure features In-Reply-To: <4A4CCE69.3070306@cryst.bioc.cam.ac.uk> References: <4A4CCE69.3070306@cryst.bioc.cam.ac.uk> Message-ID: <4A4CD003.3010005@cryst.bioc.cam.ac.uk> > Hello there, > > just a quick note to say that I am using Jalview for annotating > structural features of proteins using my own feature files. The kinds of > things that I am annotating include interactions with small molecules as > extracted from Credo > (http://www3.interscience.wiley.com/journal/121654603/abstract). Jalview > has proven a very useful tool for doing this kind of thing. It did take > a little while to get my first feature file accepted by the program > because of the lack of error messages. Also, I need to replace > disordered residues with X's so that the residue numbers match the > sequence numbers. That said, my co-workers seem to to find the results > useful. > > Cheers, > > Will > > -- Dr Will Pitt Visiting Research Associate Cambridge University Department of Biochemistry 80 Tennis Court Road Cambridge CB2 1GA UK 44(0)1223 766031 From jimp at compbio.dundee.ac.uk Thu Jul 9 10:02:45 2009 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Thu, 09 Jul 2009 10:02:45 +0100 Subject: [Jalview-discuss] Protein structure features In-Reply-To: <4A4CD003.3010005@cryst.bioc.cam.ac.uk> References: <4A4CCE69.3070306@cryst.bioc.cam.ac.uk> <4A4CD003.3010005@cryst.bioc.cam.ac.uk> Message-ID: <4A55B235.5050709@compbio.dundee.ac.uk> Hi Will. Glad to hear that Jalview has been useful here - annotation is one of its primary uses, so its great to get some feedback. William Ross Pitt wrote: >> has proven a very useful tool for doing this kind of thing. It did take >> a little while to get my first feature file accepted by the program >> because of the lack of error messages. I understand your point here - error messages are output to the console, but of course - they should be reported in a dialog box, and should be a little more informative. Also, I need to replace >> disordered residues with X's so that the residue numbers match the >> sequence numbers. Ok. Perhaps we should talk more off list about this. It sounds like you need to work with UNIPROT sequences directly rather than import the sequences directly from the PDB file (in which case, only residues with an alpha carbon will be used to construct the sequence). That said, my co-workers seem to to find the results >> useful. Great! Thanks Jim. -- ------------------------------------------------------------------- J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. From Choi at Biology.Rutgers.Edu Fri Jul 10 20:01:23 2009 From: Choi at Biology.Rutgers.Edu (Sang Chul Choi) Date: Fri, 10 Jul 2009 15:01:23 -0400 Subject: [Jalview-discuss] Can I delete columns with no variation? Message-ID: <3A903A19-24BC-42C3-931E-7B6540FE9159@Biology.Rutgers.Edu> Hi, I have a couple of questions. I am wondering if I can delete columns with no variation. I also want to know if I could know the nucleotide percentage for each site. Is there a function in Jalview to do the four gamete test? Thank you, Sang Chul From jimp at compbio.dundee.ac.uk Sat Jul 11 11:10:48 2009 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Sat, 11 Jul 2009 11:10:48 +0100 Subject: [Jalview-discuss] Can I delete columns with no variation? In-Reply-To: <3A903A19-24BC-42C3-931E-7B6540FE9159@Biology.Rutgers.Edu> References: <3A903A19-24BC-42C3-931E-7B6540FE9159@Biology.Rutgers.Edu> Message-ID: <4A586528.1090706@compbio.dundee.ac.uk> Hello Sang Chul. Sang Chul Choi wrote: > I am wondering if I can delete columns > with no variation. At this moment, you cannot - but I hope to introduce that functionality in the next version. I also want to know if I could know the nucleotide > percentage for each site. Do you mean the proportion of each base at each site ? Once again I have to say no, for the moment. Jalview calculates the percentages internally when it creates the consensus histogram, but it doesn't show the full profile to the user. Again, I think this will be introduced in the next release. > Is there a function in Jalview to do the four gamete test? Once again, no. Jalview's nucleotide analysis functions are very primitive - if you can find another way to perform the test, then you could create an annotation file to load back onto your sequences (or alignments) so Jalview could view them. Have a look in the help documentation to see details of the file formats. I hope this helps Jim. From yn_jiang at mail.utexas.edu Mon Jul 13 22:33:12 2009 From: yn_jiang at mail.utexas.edu (Yanan Jiang) Date: Mon, 13 Jul 2009 16:33:12 -0500 Subject: [Jalview-discuss] RNA Multiple sequence alignment Message-ID: <9f0fbcc50907131433w515ebees33cc5cdc0893c5ea@mail.gmail.com> Hi James, I am doing RNA multiple sequence alignment and find Jalview is a very handy tool. It seems to me that the programs (ClustalW, maffet and muscle) implemented in Jalview only have the amino acids scoring matrix. But when I called these programs, they happened to align the RNA sequences, except for muscle. Does it mean that Jalview can do RNA sequence alignment? I'm also curious about whether jalview is friendly to RNA or not. Are there some research groups using Jalview for RNA study? Thanks! Yanan -- Yanan Jiang Graduate Student Institute of Cell and Molecular Biology University of Texas at Austin From jimp at compbio.dundee.ac.uk Tue Jul 14 09:34:50 2009 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue, 14 Jul 2009 09:34:50 +0100 Subject: [Jalview-discuss] RNA Multiple sequence alignment In-Reply-To: <9f0fbcc50907131433w515ebees33cc5cdc0893c5ea@mail.gmail.com> References: <9f0fbcc50907131433w515ebees33cc5cdc0893c5ea@mail.gmail.com> Message-ID: <4A5C432A.60706@compbio.dundee.ac.uk> Hello Yanan - thanks for your nice email! Yanan Jiang wrote: > I am doing RNA multiple sequence alignment and find Jalview is a very > handy tool. That's good to hear! > But when I called these programs, they happened to align the RNA > sequences, except for muscle. Does it mean that Jalview can do RNA > sequence alignment? Muscle is designed purely for amino acid alignment, and so will only align RNA if it does not include uracil, and, as you surmised, will in any case only apply an amino acid substitution matrix. The situation is a little better with MAFFT and ClustalW - both will align RNA happily, and MAFFT in particular will also use the identity matrix to calculate substitution cost rather than an amino acid score matrix. I'm also curious about whether jalview is friendly > to RNA or not. Jalview isn't 'unfriendly' to RNA, but it doesn't have all the tools that someone working on RNA might like. In particular, there is no real support for RNA secondary structure annotation. Hopefully this will be somewhat remedied in the future, since RNA analysis is one of the focus areas in the next phase of Jalview development (which will start in a few months time). > Are there some research groups using Jalview for RNA study? There are two or three groups that I know of and are in contact with, and I also noticed that one of the citations for the new Jalview paper concerned RNA analysis. If you are interested in helping improve Jalview for RNA work, then please watch the Jalview website and announcements list, try out the new features when they appear, and tell us what you think! all the best - and I hope we'll hear from you again in the future, Jim. -- ------------------------------------------------------------------- J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. From pmberube at MIT.EDU Wed Jul 15 21:40:23 2009 From: pmberube at MIT.EDU (Paul Berube) Date: Wed, 15 Jul 2009 16:40:23 -0400 Subject: [Jalview-discuss] Problem with adjusting memory usage on MacOS version Message-ID: <2DE8B755-5C2A-4060-A0D9-004A0455E374@mit.edu> I'm having a problem adjusting the memory settings for Jalview. I'm running Jalview 2.4 on MacOS 10.5.7 (installed using installAnywhere). The program works fine except that I get a low memory error when trying to export to PNG or EPS files. Neither the Jalview.app/Contents directory nor the Info.plist file were installed. Am I missing something, or is there another file in the 2.4 version that you need to change to adjust the memory settings? Thanks, Paul For reference: Instructions for changing memory settings with MacOS version.... The lines you need to change are in the Info.plist file inside the Jalview.app/Contents directory (which is where the installAnywhere installation was made) : ! -Xms2M ! -Xmx64M Exchange the above two string tags for : -Xms500M -Xmx1000M For you information, these are the directories and files that were installed in the Jalview directory: -------------------------------------- README_IA Uninstall_Jalview Uninstall Jalview installvariables.properties InstallScript.iap_xml LICENSE output.txt lib xml-apis.jar xercesImpl.jar vamsas-client.jar wsdl4j.jar saaj.jar regex.jar mail.jar log4j-1.2.8.jar Jmol-11.0.2.jar jhall.jar jaxrpc.jar commons-logging.jar commons-discovery.jar castor-1.1-cycle-xml.jar axis.jar activation.jar jalview.jar Jalview building.html -------------------------------------- _______________________________________ Paul M. Berube Postdoctoral Associate Chisholm Laboratory Massachusetts Institute of Technology Department of Civil and Environmental Engineering _______________________________________ From jimp at compbio.dundee.ac.uk Thu Jul 16 16:55:59 2009 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Thu, 16 Jul 2009 16:55:59 +0100 Subject: [Jalview-discuss] Problem with adjusting memory usage on MacOS version In-Reply-To: <99684622-8C77-4EBD-AA36-1ACCBDC360A1@MIT.EDU> References: <2DE8B755-5C2A-4060-A0D9-004A0455E374@mit.edu> <4A5F069E.7080109@compbio.dundee.ac.uk> <32469C35-7184-4F2C-BC60-D24016D49402@MIT.EDU> <4A5F2A9D.8050008@compbio.dundee.ac.uk> <99684622-8C77-4EBD-AA36-1ACCBDC360A1@MIT.EDU> Message-ID: <4A5F4D8F.7000900@compbio.dundee.ac.uk> Paul Berube wrote: > Thanks Jim. The first option worked. > > The Jalview file is actually a package. Using the "Show package > contents" command brings up the directory containing the Info.plist > file. I made the changes to the memory settings and all seems to be > working well so far. excellent. Fingers crossed you won't get hit by the Mac java update bug! happy jalviewing! Jim. From Rachel.Hawken at csiro.au Fri Jul 17 20:54:55 2009 From: Rachel.Hawken at csiro.au (Rachel.Hawken at csiro.au) Date: Sat, 18 Jul 2009 05:54:55 +1000 Subject: [Jalview-discuss] obtaining conservation data using command line Message-ID: <1FACF94321758D4887F59BB6AE05F821665E765D22@EXNSW-MBX03.nexus.csiro.au> Hi, I am a new user to Jalview. I would like to pull out the conservation information from a multiple sequence alignment using the command line. I have installed Jalview via the java webstart. when I use the command line arguments: -open cfos.fasta -nodisplay -jalview out.txt I get an application error. 'unable to launch application' and these details: InvalidArgumentException[ Invalid arguments supplied: {out.txt, http://www.jalview.org/webstart/jalview.jnlp }] at com.sun.javaws.Main.launchApp(Unknown Source) at com.sun.javaws.Main.continueInSecureThread(Unknown Source) at com.sun.javaws.Main$1.run(Unknown Source) at java.lang.Thread.run(Unknown Source) How can I use the command line version of jalview to create the jalview output containing conservation information without manually running jalview and exporting? thanks for your help. cheers Rachel From jimp at compbio.dundee.ac.uk Tue Jul 21 18:02:01 2009 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue, 21 Jul 2009 18:02:01 +0100 Subject: [Jalview-discuss] obtaining conservation data using command line In-Reply-To: <1FACF94321758D4887F59BB6AE05F821665E765D22@EXNSW-MBX03.nexus.csiro.au> References: <1FACF94321758D4887F59BB6AE05F821665E765D22@EXNSW-MBX03.nexus.csiro.au> Message-ID: <4A65F489.5070601@compbio.dundee.ac.uk> Hello Rachel, thanks for your email. Rachel.Hawken at csiro.au wrote: > Hi, > I am a new user to Jalview. > I would like to pull out the conservation information from a multiple sequence alignment using the command line. I'm afraid there's no easy way of doing this from the command line without some kind of additional coding - however, read on. > I have installed Jalview via the java webstart. > > when I use the command line arguments: > -open cfos.fasta -nodisplay -jalview out.txt > I get an application error. 'unable to launch application' and these details: > > InvalidArgumentException[ Invalid arguments supplied: {out.txt, http://www.jalview.org/webstart/jalview.jnlp }] > at com.sun.javaws.Main.launchApp(Unknown Source) > at com.sun.javaws.Main.continueInSecureThread(Unknown Source) > at com.sun.javaws.Main$1.run(Unknown Source) > at java.lang.Thread.run(Unknown Source) This is a problem with the version of webstart that you are using - and the Jalview FAQ needs to be updated to reflect this. Many versions of webstart now do not parse on the remaining arguments to the application's main method. If you want to run jalview from the command line, the simplest route is to download the jars from here: http://www.jalview.org/webstart/ and then, assuming you have a working java on your path, and after first replacing $WSDIR with the directory where you saved the jars, use the following command: java -djava.ext.dirs=$WSDIR jalview.bin.Jalview (command line args...) > How can I use the command line version of jalview to create the jalview output containing conservation > information without manually running jalview and exporting? the above should be sufficient to execute the 'output as Jalview project file' command that you suggest above. I presume you already have the necessary parser to extract the annotation from the jalview XML file. all the best - I hope this helps Jim. From semoore at mail.ucf.edu Tue Jul 21 19:25:31 2009 From: semoore at mail.ucf.edu (Sean Moore) Date: Tue, 21 Jul 2009 14:25:31 -0400 Subject: [Jalview-discuss] A New User Has Export/Print Problems Message-ID: <89AFCF78-D568-4954-B3C4-6127A214795D@mail.ucf.edu> Hello, I would like to export a high-quality image of an alignment and consensus. In your documentation, it states that I simply File- Print. UNder the JalView File menu, there is no print option, and under the Safari (Mac OSX) file menu, print is greyed out. Am I missing something obvious? Thanks in Advance, Sean From jimp at compbio.dundee.ac.uk Wed Jul 22 17:24:29 2009 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Wed, 22 Jul 2009 17:24:29 +0100 Subject: [Jalview-discuss] A New User Has Export/Print Problems In-Reply-To: <89AFCF78-D568-4954-B3C4-6127A214795D@mail.ucf.edu> References: <89AFCF78-D568-4954-B3C4-6127A214795D@mail.ucf.edu> Message-ID: <4A673D3D.30103@compbio.dundee.ac.uk> Hi Sean. Sean Moore wrote: > I would like to export a high-quality image of an alignment and > consensus. In your documentation, it states that I simply File- > Print. UNder the JalView File menu, there is no print option, and > under the Safari (Mac OSX) file menu, print is greyed out. Am I > missing something obvious? It sounds like you are viewing your alignment on a web page through the Jalview lite applet, which cannot generate figures because it does not have access to your computer's printing or file system. You have two options: 1. If you can see it, use the 'View in full application' option in the Jalview file menu (this is only available from some web servers). 2. Save your alignment, any features and annotation using the options in the File menu. Download and run the full application from www.jalview.org/download.html, load your alignment and add in the annotation and features (you may have to edit the sequence features settings to ensure the colouring is the same). Then follow the instructions to print the alignment. I hope this helps Jim. -- ------------------------------------------------------------------- J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. From semoore at mail.ucf.edu Fri Jul 24 17:06:19 2009 From: semoore at mail.ucf.edu (Sean Moore) Date: Fri, 24 Jul 2009 12:06:19 -0400 Subject: [Jalview-discuss] Can I change the color of the "Conserved" Bar labels to something other than gold? Message-ID: <808D098D-A3AC-4862-A3F2-D94C520634BD@mail.ucf.edu> Hello, I would like to change the color of the text under the bar graphs of the Conserved bar graph so I can read them, distinguishing between a "+" and a "*" with yellow text on a white background is hard for an old man. -Sean From juettemann at gmail.com Sat Jul 25 20:26:12 2009 From: juettemann at gmail.com (Thomas Juettemann) Date: Sat, 25 Jul 2009 12:26:12 -0700 Subject: [Jalview-discuss] Newbie: Exception: java.lang.ClassNotFoundException: jalview.bin.JalviewLite Message-ID: <38f68f300907251226v18a9cc0ue93767ad1c34af5d@mail.gmail.com> Dear all, I am trying to implement the jalview applet and keep getting this error: java.lang.ClassNotFoundException: jalview.bin.JalviewLite at sun.plugin2.applet.Applet2ClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at sun.plugin2.applet.Plugin2ClassLoader.loadCode(Unknown Source) at sun.plugin2.applet.Plugin2Manager.createApplet(Unknown Source) at sun.plugin2.applet.Plugin2Manager$AppletExecutionRunnable.run(Unknown Source) at java.lang.Thread.run(Unknown Source) Caused by: java.io.IOException: open HTTP connection failed:http://bisc.cse.ucsc.edu/jalview/bin/JalviewLite.class at sun.plugin2.applet.Applet2ClassLoader.getBytes(Unknown Source) at sun.plugin2.applet.Applet2ClassLoader.access$000(Unknown Source) at sun.plugin2.applet.Applet2ClassLoader$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) ... 7 more Exception: java.lang.ClassNotFoundException: jalview.bin.JalviewLite This is the page I am trying it: http://bisc.cse.ucsc.edu/testjview.html And this is the source code: JalView Test Click the Javascript buttons below to interact with the Applet instance on the page.
View the source in your browser to see how it has been done.
I am not very experienced with either Java nor applets. -rwxrwxr-x jalviewApplet.jar Any suggestions more than welcome! Many thanks, Thomas From michael.wilson at bbsrc.ac.uk Wed Jul 29 12:35:37 2009 From: michael.wilson at bbsrc.ac.uk (michael wilson (BI)) Date: Wed, 29 Jul 2009 12:35:37 +0100 Subject: [Jalview-discuss] gi to uniprot?? Message-ID: HI All!! I really like the Jalview editor, but I often have multisequence fasta files which have protein id from ncbi. This doesn't allow me to use the links to info about the protein that are available with uniport ids. Is there some way I can make the links from gi| to uniport in Jalview, without doing a manual lookup up and translate?? Many thank yous to anyone that can help me in this regard. If this was automatically done by Jalview, it would, indeed, be perfect. CHEERS! Michael