Re: [Jalview-discuss] Feature

Hello Päivi, We can reproduce this problem and have a couple of alternative code fixes to assess in order to resolve it. I will let you know when the fix is published - probably this Friday (12th Dec). Best regards, Mungo Carstairs Division of Computational Biology University of Dundee

Re: [Jalview-discuss] Problems to use Jalview in my Mac OS 10.6.8

://www.compbio.dundee.ac.uk/ From: Toni Aliaga toal...@gmail.com Sent: 28 January 2015 12:12 To: Mungo Carstairs (Staff) Subject: Re: [Jalview-discuss] Problems to use Jalview in my Mac OS 10.6.8 Hello Mungo, I tried several ways but I am trying to launch the 'launch desktop

Re: [Jalview-discuss] Problems to use Jalview in my Mac OS 10.6.8

?Hello Toni, Can you describe the problems you are having? How are you trying to launch Jalview, and what errors are you seeing? If Jalview starts, can you capture the contents of the Java Console window (Tools | Show Java Console)? Thanks, Mungo Carstairs Jalview Computational Scientist

Re: [Jalview-discuss] Coloring error

Hi Engin, This is indeed a bug which we will fix in the next release. Meanwhile a workaround is to select the 'Case Sensitive' option in the colour chooser dialog. (There is no need to pick colours for lower case unless your sequences include lower case characters.) Thanks, Mungo Mungo

Re: [Jalview-discuss] No longer able to launch Jalview on Mac

Hi Matteo, There is an FAQ for this question at http://www.jalview.org/faq (or directly at http://www.jalview.org/node/53?) Please look over this and let us know if it helps resolve your problem. Thanks! Mungo Mungo Carstairs Jalview Computational Scientist The Barton Group Division of

Re: [Jalview-discuss] No longer able to launch Jalview on Mac

To: Mungo Carstairs (Staff) Cc: Ricardo R Gonzalez Mendez Subject: Re: No longer able to launch Jalview on Mac Hi Mungo and Ricardo, Thank you for the prompt reply. I deleted the current Jalview app and downloaded a new one from the link you provided, and that seems to have solved the problem. Thanks

Re: [Jalview-discuss] JalView 3D Protein Alignment

Carstairs (Staff) Subject: RE: [Jalview-discuss] JalView 3D Protein Alignment Hi Mungo, Yes that is the same behavior I am seeing, can I overlay all four if I do them one at a time? Thanks, Kathleen From: g.m.carsta...@dundee.ac.uk To: jalview-discuss@jalview.org

Re: [Jalview-discuss] Bug in annotation file parser

Hello Arne, Thanks for reporting this and providing such a clear example. It does look like a bug, whose root cause is that the code is trying to interpret the display text of the annotation as if it were 'e' as in RNA secondary structure (E-e) base pair notation. (The bug also occurs with

Re: [Jalview-discuss] Windows 2 error

. uninstall Java 2. Download the software package that comes with Java 3. if there are problems with other software because of this then re-download Java independently of the software. Sincerely, Gary Jones Sent from Surface From: Mungo Carstairs (Staff)<mailto:g.m.carsta...@dundee.ac.uk> Se

Re: [Jalview-discuss] Error loading file message

Hello Adeba, Are these files sequence data, Jalview project files, or other? Can you open the Java console from Jalview (Tools | Open Java Console) and report the information displayed there please, including Jalview and Java version, operating system, and any error message. If you want to

Re: [Jalview-discuss] Error loading file message

, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> From: Adeba Mohammad <amoham...@westernu.edu> Sent: 07 January 2016 13:30 To: Mungo Carstairs (Staff) Subject: Re: [Jalv

Re: [Jalview-discuss] Can't open Jalview

Hello Pedro, What version of OSX operating system and Java (type "java -version" in a terminal window) are you running? Are you able to open a terminal window in the Jalview installation directory (typically /Applications/Jalview/Jalview.app/Contents/MacOS) and run it directly with

Re: [Jalview-discuss] Can't open Jalview

ro Gonçalves <antoniopedrocard...@gmail.com> Sent: 22 December 2015 18:19 To: Mungo Carstairs (Staff) Subject: Re: [Jalview-discuss] Can't open Jalview Hello Mungo, java version "1.6.0_65" Java(TM) SE Runtime Environment (build 1.6.0_65-b14-462-11M4609) Java HotSpot(TM) 64-Bit Se

Re: [Jalview-discuss] Delete non-gap sites in linked split frame view?

of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> From: Povilus, Rebecca Ann <rpovi...@fas.harvard.edu> Sent: 07 January 2016 18:12 To: Mungo Carstairs (Staff

Re: [Jalview-discuss] Incorrect feature mapping on gapped sequencs

Hello David, I have loaded up your example and what I see is: - columns 8289-8295 show feature located on bases 8093-8099 of the sequence (positions confirmed in the status bar) - columns 8475-8481 show feature located on bases 8279-8285 " " " " " " " 'Remove all gaps' and the feature

Re: [Jalview-discuss] Jalview.jnlp on ubuntu

is below. openjdk version "1.8.0_92" OpenJDK Runtime Environment (Zulu 8.15.0.1-linux64) (build 1.8.0_92-b15) OpenJDK 64-Bit Server VM (Zulu 8.15.0.1-linux64) (build 25.92-b15, mixed mode) Thanks, Ganesh On 7 Feb 2017, at 17:54, Mungo Carstairs (Staff) <g.m.carsta...@dundee.ac.uk

Re: [Jalview-discuss] Fwd: Re: Fwd: Color by secondary structure

Just a detail, but you also need to ensure that in Tools | Preferences, under Structure, the options - Process secondary structure from PDB - Add secondary structure annotation to alignment are selected (and add Temperature Factor if of interest). Mungo Mungo Carstairs Jalview

Re: [Jalview-discuss] Problem in DAS registry

Hello Chengji, Unfortunately the EBI's static mirror copy of the original Sanger-hosted DAS registry is no longer available. To the best of our knowledge there is no alternative site that now provides this. If this changes we will let Jalview users know! Sorry for any inconvenience (but it

Re: [Jalview-discuss] Problems installing and then running Jalview on Windows 10

Hello Kausik, As a workaround, are you able to edit the jnlp file that is downloaded for Jalview Webstart to increase max-heap-size say to 2G? And run from the command line with javaws. Someone will follow up on the Installer error (who is not on a mini iPad in a remote corner of the Scottish

Re: [Jalview-discuss] unsubscribe

Hi, Please use the unsubscribe link at the foot of this page: http://www.jalview.org/mailman/listinfo/jalview-discuss Thanks, Mungo Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee,

Re: [Jalview-discuss] out of memory

of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> From: Yizhuang Zhou <zhouyizhua...@163.com> Sent: 06 January 2017 09:43:26 To: Mungo Carstairs (Staff); jal

Re: [Jalview-discuss] Fw:

Hi Maheen, Sorry to hear you are having problems. Can you confirm if it is the Jalview installer, or Jalview itself, that is failing to open. What error message(s) do you get when you try this from the command line? Thanks, Mungo Mungo Carstairs Jalview Computational Scientist The

Re: [Jalview-discuss] could not open JALview in MacOS Sierra

Hello Sirin, We have some outstanding issues with code certificate signing for OSX to work through. Meanwhile it should be possible for you to launch the WebStart version of Jalview. Either click on 'Launch Jalview Desktop' at http://www.jalview.org/, or launch Webstart 'Latest official

Re: [Jalview-discuss] some links on the www.jalview.org are broken

sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 From: Wang, Haibin (CDC/OID/NCIRD) (CTR) <y...@cdc.gov> Sent: 31 May 2017 14:27:22 To: Mungo Carstairs (Staff); ja

Re: [Jalview-discuss] truncated image eps format

Hello Muhammad, I've done some investigation into this problem. It turns out that the EPS file produced by Jalview is correctly formed, but the image is too large to be fully rendered by some external viewers. For example, an alignment with 2000 columns gives an EPS image which is truncated

Re: [Jalview-discuss] sequence feature in Jalview

Hello Vera, If I understand your question, you have loaded alignment data from local files (e.g. Fasta) and would like to retrieve Uniprot annotation for these. You can do this from Jalview menu option Web Services | Fetch DB References | Standard Databases (or select Uniprot) Note for

Re: [Jalview-discuss] sequence feature in Jalview

tp://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 _

Re: [Jalview-discuss] Changing Protein to Nucleotide Sequence

Hello Vaish, Two good questions there! The short answer is no, not at present, but we can bump and/or raise feature requests for these. Protein / Nucleotide You are right, Jalview 'guesses' nucleotide if the alignment is more than 85% ACGTU - and this doesn't work well with lots of N's.

Re: [Jalview-discuss] Changing Protein to Nucleotide Sequence

g-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ________ From: jalview-discuss-boun...@jalview.org on behalf of Mungo Carstairs (Staff) Sent: 14 June 2018 09:59:19 To: Vonyx Crystal; jalview-discuss@jalview.org Subject: Re: [Jalview-discuss]

Re: [Jalview-discuss] Jabaws server offline

Hi, Yes, Jabaws servers are currently down as a result of a weekend power failure. Servers are in the process of being restarted - will advise when available again. Thanks, Mungo [University of Dundee shield logo] Mungo Carstairs Jalview Computational

Re: [Jalview-discuss] Can't stop long-running tree calculation

Hi Chris, Unfortunately not - the calculation runs in a separate thread and is not currently designed to be interruptible or cancellable. Your choices are limited to wait for completion, or kill Jalview completely. Mungo [University of Dundee shield logo]

Re: [Jalview-discuss] Jalview properties file : documentation ?

Though I notice another gui Preference, to specify a fixed id width, doesn't work: it is saved against "FIGURE_USERIDWIDTH", but the code looks for "FIGURE_FIXEDIDWIDTH" . mungo [University of Dundee shield logo] Mungo Carstairs Jalview Computational Scientist

Re: [Jalview-discuss] Retrieve score for conservation at the individual amino acid level

____ From: Geoffrey Barton (Staff) Sent: 27 November 2018 23:32:03 To: Mungo Carstairs (Staff); jalview-discuss@jalview.org; Romain Studer Subject: Re: [Jalview-discuss] Retrieve score for conservation at the individual amino acid level Hi Romain, If it is just the

Re: [Jalview-discuss] Retrieve score for conservation at the individual amino acid level

Hi Romain, I'm not quite sure if you want conservation scores, or BLOSUM scores, or both... 'Colour by Conservation' uses conservation score to 'fade' whatever colour scheme is selected. http://www.jalview.org/help/html/colourSchemes/conservation.html The conservation score is per column

Re: [Jalview-discuss] Retrieve score for conservation at the individual amino acid level

Hi Romain, Try running the attached script in the Jalview Groovy console - it should output residue Blosum62 scores against the alignment consensus. Regards, Mungo [University of Dundee shield logo] Mungo Carstairs Jalview Computational Scientist The Barton

Re: [Jalview-discuss] How to plot hydrophobicity in multiple sequence alignment

____ From: jalview-discuss-boun...@jalview.org on behalf of Mungo Carstairs (Staff) Sent: 22 March 2019 13:41:02 To: Dr. Rohit Jain; jalview-discuss@jalview.org Subject: Re: [Jalview-discuss] How to plot hydrophobicity in multiple sequence alignment Hello Rohit, I've attached a groo

Re: [Jalview-discuss] How to plot hydrophobicity in multiple sequence alignment

Hello Rohit, I've attached a groovy script that can be run to produce average hydrophobicity score annotation (copying in the list now we know it works for you!). Tools | Groovy console | paste in the script and Script | Run. I recommend choosing Jalview option Annotations | Autocalculated

Re: [Jalview-discuss] Jalview Freezing

Hello Dave, Any errors showing in the Java console? Does your ~/.jalview_properties file have a line RELAXEDSEQIDMATCHING=true - if so, you try removing this. It may trigger some highly nested 'fuzzy matching' of sequence ids (in the features file) to ids or cross-references of sequences

Re: [Jalview-discuss] Export fails for big alignment

Hello Ahmad, Can you please confirm * the output image format (e.g. EPS) and file size * how you are trying to open it (e.g. OSX Preview, Adobe Illustrator, other) * any error message you can see when trying to open the file We have seen problems in the past due to MAC's Preview

Re: [Jalview-discuss] load annotations or future file

ee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ____ From: Nail Besli Sent: 02 July 2019 13:37:50 To: Mungo Carstairs (Staff) Subject

Re: [Jalview-discuss] how to see species names

Hello Roisin, Could you explain a bit more "I can't get JalView to allow me to see them."? Is there an error happening, or is it just that the names are too long to see? If the latter, you can drag the name panel to be wider - put the cursor just above the top sequence name until it changes

[Jalview-discuss] Ensembl services maintenance today

Please note that Ensembl are carrying out server maintenance today. As a result there will be a period when requests from Jalview to fetch Ensembl data fail. Normal service should be resumed later today. Mungo [University of Dundee shield logo] Mungo Carstairs

Re: [Jalview-discuss] Web services issue

July 2019 10:41:39 To: jalview-discuss@jalview.org; James Procter (Staff); Mungo Carstairs (Staff) Subject: Web services issue I'm trying to align some DNA sequences but the web services gives an error. Both Muscle and Clustal. File attached. Is there a server error? ..d Dr David Martin Sen

Re: [Jalview-discuss] load annotations or future file

Hello Nail, I am sorry to hear you are having problems. An annotation or features file should be plain text format, not JSON. Please see the help pages in the application or at http://www.jalview.org/help/html/features/annotationsFormat.html

Re: [Jalview-discuss] Problem with sequence features file

] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ____ From: Atkinson, Samantha Sent: 24 July 2019 17:29:50 To: Mungo Carstairs (Staff) ; jalview-dis

Re: [Jalview-discuss] how to see species names

_________ From: roisin mcallister Sent: 05 July 2019 16:38:28 To: Mungo Carstairs (Staff) Subject: Re: [Jalview-discuss] how to see species names Hi Mungo thanks for speedy reply! No error and I have pulled the panel out wider. I attach so you can see what I mean. The species na

Re: [Jalview-discuss] Help needed - Marking up a list of peptides onto a protein alignment

] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ____ From: jalview-discuss-boun...@jalview.org on behalf of Mungo Carstairs (Staff) Sent: 26

Re: [Jalview-discuss] Help needed - Marking up a list of peptides onto a protein alignment

] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ____ From: jalview-discuss-boun...@jalview.org on behalf of Mungo Carstairs (Staff) Sent: 24

Re: [Jalview-discuss] Help needed - Marking up a list of peptides onto a protein alignment

Hello Manoj, Thanks for getting in touch. Let me check I have understood what you are aiming for. Jalview lets you search any alignment for any sequence motif (which could be an exact match or a regular expression pattern). You can search for all matches, and create sequence features on the

Re: [Jalview-discuss] Help needed - Marking up a list of peptides onto a protein alignment

stagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ____ From: jalview

Re: [Jalview-discuss] load annotations or future file

y of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ________ From

Re: [Jalview-discuss] How to change numbering on my alignment?

Hello Kate, I'm not quite sure what the question is, so I'll answer two ways. You can change the order of sequences in the alignment by clicking on the sequence name and dragging them up or down. You can change the start position of a sequence by right-clicking on the name, and following the