From j.richer3 at mycanadore.ca Wed Feb 1 15:08:31 2012 From: j.richer3 at mycanadore.ca (Jessie Richer) Date: Wed, 1 Feb 2012 15:08:31 +0000 Subject: [Jalview-discuss] help .. jalview wont move past "queuing" page Message-ID: <7731109D1174054B9841B10171FD0D640E2F8E86@BY2PRD0510MB352.namprd05.prod.outlook.com> Hello I am having a problem with JalView (the install anywhere version). I have a big fasta file (nearly 5MB) and when I go to align the sequences through the Web Alignment tab (I am using Clustal w. defaults) the dialog box pops up, but does not leave the "align with ClustalWS - queuing" page.. This has been running almost two hours. I have used this before for another set of sequences (almost 2MB fasta file) and had no problems, although it did take about an hour to load. I Have triied redoing this same sequences but am still getting the same "align with clustalWS - queuing" page, and it wont move past this point.. I read on increasing the size.. making a backup of a file in program file, but unfortunatly I can not do this as I am using my unviersities computers and they have the admin portions blocked out and I can not access the admin username and password. Help! Any ideas why it will not move past the queuing page? is there a size limit to the fasta file? Could there be a problem with the CLustal program that is not allowing me to move forward? Any Help would be greatly appreciated and as soon as possible so I can continue to move forward.. Thanks!! Jess -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20120201/9bbdd378/attachment.html From jprocter at compbio.dundee.ac.uk Wed Feb 1 16:35:20 2012 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Wed, 01 Feb 2012 16:35:20 +0000 Subject: [Jalview-discuss] help .. jalview wont move past "queuing" page In-Reply-To: <7731109D1174054B9841B10171FD0D640E2F8E86@BY2PRD0510MB352.namprd05.prod.outlook.com> References: <7731109D1174054B9841B10171FD0D640E2F8E86@BY2PRD0510MB352.namprd05.prod.outlook.com> Message-ID: <4F2969C8.3000002@compbio.dundee.ac.uk> Hi there, Jessie. On 01/02/2012 15:08, Jessie Richer wrote: > > I have a big fasta file (nearly 5MB) and when I go to align the > sequences through the Web Alignment tab (I am using Clustal w. > defaults) the dialog box pops up, but does not leave the "align with > ClustalWS - queuing" page.. This has been running almost two hours. > ah - you are not the only one to notice this! We had a busy time today on our cluster, which revealed some configuration issues with the new JABAWS 2.0 server that Jalview now uses. These have been fixed now, so hopefully your jobs will complete soon. > I have used this before for another set of sequences (almost 2MB fasta > file) and had no problems, although it did take about an hour to > load. I Have triied redoing this same sequences but am still getting > the same "align with clustalWS - queuing" page, and it wont move past > this point.. > The version of ClustalW that Jalview uses will take a bit of time with 5MB of sequences. You might actually get a good alignment in less time if you use the MAFFT service. If they are proteins, then you could also try out Clustal Omega (ClustalO) which is extremely fast and accurate, and already available in the development version of jalview here: http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/develop/webstart/jalview_2G.jnlp > > I read on increasing the size.. making a backup of a file in program > file, but unfortunatly I can not do this as I am using my unviersities > computers and they have the admin portions blocked out and I can not > access the admin username and password. > Yes. If you are using a locally installed version of Jalview you do need to have admin rights to change the memory allocation. However, you should be able to run the webstart version of Jalview with different memory options. Default memory settings: http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/develop/webstart/jalview.jnlp 1 gig of memory: http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/develop/webstart/jalview_1G.jnlp 2 gigs of memory: http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/develop/webstart/jalview_2G.jnlp On each of these links, you'll be ask to 'trust' the Java web start program's certificate. You need to agree to this, otherwise the program won't launch on the machine. If jalview still doesn't launch with one of the big memory links, then just use a link for a smaller memory setting. Hope this helps! Jim -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20120201/6e11cc52/attachment.html From ljgarcia at ebi.ac.uk Mon Feb 6 14:11:48 2012 From: ljgarcia at ebi.ac.uk (Leyla Garcia) Date: Mon, 06 Feb 2012 14:11:48 +0000 Subject: [Jalview-discuss] DAS Workshop - Last week for registration In-Reply-To: <3BBFA5DBCADBE54EAA730CB90E7BCDBF039FC420@SERV-MAILBOX2.igbmc.u-strasbg.fr> References: <3BBFA5DBCADBE54EAA730CB90E7BCDBF039FC420@SERV-MAILBOX2.igbmc.u-strasbg.fr> Message-ID: <4F2FDFA4.1040403@ebi.ac.uk> [Apologies for cross-posting] ============================== Last week to register for DAS Workshop 2012 DAS is currently being used to share annotations on genomes, protein alignments, structural and interaction information. If you are interested in sharing biological information the DAS workshop below may be of interest to you. Learn of and contribute to current developments in DAS such as: DAS in the cloud, DAS for Genotype Data, DAS searching, DAS for collaborative annotation projects, DAS alternative formats. Registration is open for the 2012 DAS workshop (27-29 February) at the Genome Campus, Hinxton UK. If you are interested in attending, please find out more by going to http://www.ebi.ac.uk/training/onsite/120227_DAS.html and register via the web link at the bottom of the page. This workshop will cater for novice to expert DAS users as each day is optional. Please register early as places will be limited. Registration closes 10 February 2012 - 12:00. If you are interested in giving a 15 minute talk on the second day please email Jonathan Warren using jonathan.warren at sanger.ac.uk Many thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20120206/c05704e1/attachment.html From j.richer3 at mycanadore.ca Tue Feb 7 13:11:32 2012 From: j.richer3 at mycanadore.ca (Jessie Richer) Date: Tue, 7 Feb 2012 13:11:32 +0000 Subject: [Jalview-discuss] help Message-ID: <7731109D1174054B9841B10171FD0D640E2F8FCF@BY2PRD0510MB352.namprd05.prod.outlook.com> I need help fixing and/or diagnosing this problem: My colour for percentage identity isnt working! I aligned the sequences using CLustal with defaults.. then clicked on colour and percentage identity but no colour shows up and there should be considering this set of sequences have 3 T in a row across all 7 sequences. The little circle is beside percentage identity but no colour appears.. I need help as soon as possible please! Thanks! Jess -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20120207/8ed7e763/attachment.html From jprocter at compbio.dundee.ac.uk Tue Feb 7 14:21:27 2012 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Tue, 07 Feb 2012 14:21:27 +0000 Subject: [Jalview-discuss] help In-Reply-To: <7731109D1174054B9841B10171FD0D640E2F8FCF@BY2PRD0510MB352.namprd05.prod.outlook.com> References: <7731109D1174054B9841B10171FD0D640E2F8FCF@BY2PRD0510MB352.namprd05.prod.outlook.com> Message-ID: <4F313367.7010803@compbio.dundee.ac.uk> Hello Jessie On 07/02/2012 13:11, Jessie Richer wrote: > > I need help fixing and/or diagnosing this problem: > > My colour for percentage identity isnt working! > > I aligned the sequences using CLustal with defaults.. then clicked on > colour and percentage identity but no colour shows up and there should > be considering this set of sequences have 3 T in a row across all 7 > sequences. > > The little circle is beside percentage identity but no colour appears.. > > I need help as soon as possible please! > Could you please send me a copy of your alignment and let me know which version of Jalview you are using ? (you can see it in the dialog that pops up when you select Help->About). Jim. ps. if you are using a web site to align your sequences, and your sequences are all in lower case (ie 't' not 'T'), then try selecting all the seqeunces, right clicking and following the 'Edit' submenu to select the 'To Upper case' option. This might be the cause... -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20120207/2d2cb2ec/attachment.html From j.richer3 at mycanadore.ca Tue Feb 7 14:30:31 2012 From: j.richer3 at mycanadore.ca (Jessie Richer) Date: Tue, 7 Feb 2012 14:30:31 +0000 Subject: [Jalview-discuss] help In-Reply-To: <4F313367.7010803@compbio.dundee.ac.uk> References: <7731109D1174054B9841B10171FD0D640E2F8FCF@BY2PRD0510MB352.namprd05.prod.outlook.com>, <4F313367.7010803@compbio.dundee.ac.uk> Message-ID: <7731109D1174054B9841B10171FD0D640E2F8FF7@BY2PRD0510MB352.namprd05.prod.outlook.com> Hi.. I managed to figure it out.. had to shut down jalview and restart the computer and then the colour worked again.. Now I am waiting on the sequences to align.. has said "queuing" for the last hour or so on 3 separate sets of sequences.. I had this same problem last week and it turned out there was a problem with the server or something? they did eventually finish (5 hours later).. hoping it doesnt take that long today... ________________________________ From: Jim Procter [foreveremain at gmail.com] on behalf of Jim Procter [jprocter at compbio.dundee.ac.uk] Sent: February 7, 2012 9:21 AM To: Jessie Richer Cc: jalview-discuss at jalview.org Subject: Re: [Jalview-discuss] help Hello Jessie On 07/02/2012 13:11, Jessie Richer wrote: I need help fixing and/or diagnosing this problem: My colour for percentage identity isnt working! I aligned the sequences using CLustal with defaults.. then clicked on colour and percentage identity but no colour shows up and there should be considering this set of sequences have 3 T in a row across all 7 sequences. The little circle is beside percentage identity but no colour appears.. I need help as soon as possible please! Could you please send me a copy of your alignment and let me know which version of Jalview you are using ? (you can see it in the dialog that pops up when you select Help->About). Jim. ps. if you are using a web site to align your sequences, and your sequences are all in lower case (ie 't' not 'T'), then try selecting all the seqeunces, right clicking and following the 'Edit' submenu to select the 'To Upper case' option. This might be the cause... -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20120207/b9532e7e/attachment.html From foreveremain at gmail.com Tue Feb 7 15:31:46 2012 From: foreveremain at gmail.com (Jim Procter) Date: Tue, 07 Feb 2012 15:31:46 +0000 Subject: [Jalview-discuss] help In-Reply-To: <7731109D1174054B9841B10171FD0D640E2F8FF7@BY2PRD0510MB352.namprd05.prod.outlook.com> References: <7731109D1174054B9841B10171FD0D640E2F8FCF@BY2PRD0510MB352.namprd05.prod.outlook.com>, <4F313367.7010803@compbio.dundee.ac.uk> <7731109D1174054B9841B10171FD0D640E2F8FF7@BY2PRD0510MB352.namprd05.prod.outlook.com> Message-ID: <4F3143E2.70208@gmail.com> On 07/02/2012 14:30, Jessie Richer wrote: > > Hi.. I managed to figure it out.. had to shut down jalview and restart > the computer and then the colour worked again.. > > Now I am waiting on the sequences to align.. has said "queuing" for > the last hour or so on 3 separate sets of sequences.. I had this same > problem last week and it turned out there was a problem with the > server or something? they did eventually finish (5 hours later).. > hoping it doesnt take that long today... > I do remember your email - but I don't think you ever replied to my email about using a different way of starting Jalview. If you are aligning very long sequences, you should really start Jalview with more memory. You can find out how much you have or have left by selecting the 'Show memory usage' option under the tools menu. If you have less than 50 percent when your alignment comes back from the server, I would recommend increasing the memory allocated to jalview. Jim. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20120207/6a1e8159/attachment.html From fpasin at cnb.csic.es Tue Feb 7 17:02:53 2012 From: fpasin at cnb.csic.es (Fabio) Date: Tue, 07 Feb 2012 18:02:53 +0100 Subject: [Jalview-discuss] Error - Jmol associated .pdb files Message-ID: <20120207180253.1242177h3yc7837h@webmail.csic.es> Hi Jim, I'm trying to view the structure of some sequences, but when Jmol tries to open the associated .pdb files - it's not able to locate them. The same as reported in this message http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/2011-June/000614.html from what i've seen it seems that "\" used by Windows is misinterpreted and recognized as "delete the character that follows me" thus it is not able to locate where the .pdb file is stored. I attempted to move all the .pdb files directly to C: to make it easier to locate them. It works, but when i save the project and i reopen it, Jmol looks for a temporary file and it is not able to locate it [as the same "\" problem is kept], i' don't know i'm not an informatic it happens in both Jalview 2.6, 2.7 and Development Branch [i downloaded the .jnlp from one of your previous messages] i'm using Windows XP best regards, fabio -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20120207/1f2561c4/attachment-0001.html From jprocter at compbio.dundee.ac.uk Wed Feb 8 10:26:06 2012 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Wed, 08 Feb 2012 10:26:06 +0000 Subject: [Jalview-discuss] Error - Jmol associated .pdb files In-Reply-To: <20120207180253.1242177h3yc7837h@webmail.csic.es> References: <20120207180253.1242177h3yc7837h@webmail.csic.es> Message-ID: <4F324DBE.4020403@compbio.dundee.ac.uk> Hi Fabio. I'm sorry that you've hit this bug - I'm hoping to fix it very soon. If you'd like to register on our bug tracker, you can add a watch to the bug ( http://issues.jalview.org/browse/JAL-1023 ) so you'll be notified when I get around to fixing it. Jim. On 07/02/2012 17:02, Fabio wrote: > > Hi Jim, > > I'm trying to view the structure of some sequences, but when Jmol > tries to open the associated .pdb files - it's not able to locate > them. The same as reported in this message > > http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/2011-June/000614.html > > from what i've seen it seems that "\" used by Windows is > misinterpreted and recognized as "delete the character that follows > me" thus it is not able to locate where the .pdb file is stored. I > attempted to move all the .pdb files directly to C: to make it easier > to locate them. It works, but when i save the project and i reopen it, > Jmol looks for a temporary file and it is not able to locate it [as > the same "\" problem is kept], i' don't know i'm not an informatic > > it happens in both Jalview 2.6, 2.7 and Development Branch [i > downloaded the .jnlp from one of your previous messages] > > i'm using Windows XP > > best regards, > > fabio > > > > _______________________________________________ > Jalview-discuss mailing list > Jalview-discuss at jalview.org > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20120208/d8c61a9a/attachment.html From T.G.P.Bolderink at lumc.nl Fri Feb 24 09:58:15 2012 From: T.G.P.Bolderink at lumc.nl (T.G.P.Bolderink at lumc.nl) Date: Fri, 24 Feb 2012 09:58:15 +0000 Subject: [Jalview-discuss] error on loadAlignment function Message-ID: <15561BC69C23CB41A5620BD61E6327F6248AF82C@MAIL-MB1.lumcnet.prod.intern> I have been working on passing an alignment from a website to the applet i experimented with different ways but i found one way that Works on most computers , except on some i get errors trying to open jalview (in IE its :object doesn't support this property or method and in Firefox the error is :loadAlignment is not a function). The strange thing is that an identical computer with the same browsers and versions has no errors at all and works perfectly. any ideas on what might cause this problems? code I use: (this code is used inside a perl cgi script hence the slashes and quotes) function startJalview_(title,alwvar) { alignment =\"$jalview_alignment\"; eval(\'var \'+alwvar+\' = document.JalviewLite.loadalignment(alignment,title)\'); } Things I tried: checking permissions(of all the files ) checking browser settings( eg scripts enabled) changing names/capitals, removed the var from'var alignment =\"$jalview_alignment\"; ' and made loadAlignment all lowercase( possible fixes I found on the internet). Thanks in advance, Thomas -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20120224/255340cd/attachment.html From jprocter at compbio.dundee.ac.uk Fri Feb 24 13:06:18 2012 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Fri, 24 Feb 2012 13:06:18 +0000 Subject: [Jalview-discuss] error on loadAlignment function In-Reply-To: <15561BC69C23CB41A5620BD61E6327F6248AF82C@MAIL-MB1.lumcnet.prod.intern> References: <15561BC69C23CB41A5620BD61E6327F6248AF82C@MAIL-MB1.lumcnet.prod.intern> Message-ID: <4F478B4A.2050606@compbio.dundee.ac.uk> Hi Thomas On 24/02/2012 09:58, T.G.P.Bolderink at lumc.nl wrote: > > I have been working on passing an alignment from a website to the > applet i experimented with different ways but i found one way that > Works on most computers , except on some i get errors trying to open > jalview (in IE its :object doesn't support this property or method and > in Firefox the error is :loadAlignment is not a function). > > The strange thing is that an identical computer with the same browsers > and versions has no errors at all and works perfectly. > any ideas on what might cause this problems? > This is very mysterious. Do you get similar problems with this web page: http://www.jalview.org/examples/javascriptLaunch.html Also, can you give me a URL where I can see your server from ? Jim. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20120224/af344c41/attachment.html