Hi all,
I am trying to export my msa with its structure prediction from jalview environment in eps format but the exported image is always truncated from its four sides. Is there any solution or suggestion? Many Thanks.
Hi Muhammad
I am trying to export my msa with its structure prediction from jalview
environment in eps format but the exported image is always truncated
from its four sides. Is there any solution or suggestion? Many Thanks.
Could you send me the Jalview project file and the EPS that was
generated ? Also - please send us the version of Jalview and OS that you
are running (Tools->Jalview Java Console will open a window showing this
information).
Lastly - please try with the latest Jalview version (2.10.2) - EPS
export seems to have no problems as far as we can tell, but your data
may reveal a bug.
Hear from you soon,
Jim.
···
On 21/08/2017 00:02, Muhammad Zayed wrote:
--
--
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk
Hi Muhammad
I am trying to export my msa with its structure prediction from jalview environment in eps format but the exported image is always truncated from its four sides. Is there any solution or suggestion? Many Thanks.
Thanks for sending me your alignment. I performed a secondary structure prediction and tried to export the EPS and also saw that the figure was truncated. It is definitely a bug - https://issues.jalview.org/browse/JAL-2695
As a work around, I found that if you right click on the ‘reference sequence’ - the one you performed a secondary struture prediction on, and select ‘Hide Insertions’ - you can export an EPS containing the full secondary structure prediction without it being truncated.
We’ll take a look at this - thanks very much for emailing !
Jim.
···
On 21/08/2017 20:50, Jim Procter wrote:
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
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 when viewed in (Mac) Preview, but complete when viewed with Adobe Illustrator. Your alignment (2773 columns) generates an EPS image which is truncated when viewed in either Preview or Illustrator.
Hopefully Jim’s suggestion for a workaround can help you, otherwise I’m afraid this seems to be a limitation of the EPS output format.
…unless any other Jalview users with more knowledge of image handling software than me can chip in with suggestions!
Best regards,
Mungo
···
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK
www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017
From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Jim Procter jprocter@compbio.dundee.ac.uk
Sent: 28 August 2017 11:12:42
To: jalview-discuss@jalview.org; mhdatefzayed@yahoo.com
Subject: Re: [Jalview-discuss] truncated image eps format
Hi Muhammad
On 21/08/2017 20:50, Jim Procter wrote:
On 21/08/2017 00:02, Muhammad Zayed wrote:I am trying to export my msa with its structure prediction from jalview environment in eps format but the exported image is always truncated from its four sides. Is there any solution or suggestion? Many Thanks.
Thanks for sending me your alignment. I performed a secondary structure prediction and tried to export the EPS and also saw that the figure was truncated. It is definitely a bug - https://issues.jalview.org/browse/JAL-2695
As a work around, I found that if you right click on the ‘reference sequence’ - the one you performed a secondary struture prediction on, and select ‘Hide Insertions’ - you can export an EPS containing the full secondary structure prediction without it being truncated.
We’ll take a look at this - thanks very much for emailing !
Jim.
–
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
The University of Dundee is a registered Scottish Charity, No: SC015096
Mmm. In principle, EPS should cope with anything, but as you have found, some viewers/software has limits on the total size of an image.
If this persists as a problem you might like to try the old ALSCRIPT software to make your eps files. This is more complex to use than Jalview, but will tile very large alignments over multiple EPS pages that you can then view or print separately. They are in one file though, so this may still be a problem for some software.
There is a link to the download page for ALSCRIPT here: http://www.compbio.dundee.ac.uk/software.html
You can generate the alignment format the ALSCRIPT needs from Jalview, it is blc or block file format.
Geoff.
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 when viewed in (Mac) Preview, but complete when viewed with Adobe Illustrator. Your alignment (2773 columns) generates an EPS image which is truncated when viewed in either Preview or Illustrator.
Hopefully Jim’s suggestion for a workaround can help you, otherwise I’m afraid this seems to be a limitation of the EPS output format.
…unless any other Jalview users with more knowledge of image handling software than me can chip in with suggestions!
Best regards,
Mungo
Mungo Carstairs
Jalview Computational ScientistThe Barton Group
Division of Computational BiologySchool of Life Sciences
University of Dundee, Dundee, Scotland, UK
www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017
From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Jim Procter jprocter@compbio.dundee.ac.uk
Sent: 28 August 2017 11:12:42
To: jalview-discuss@jalview.org; mhdatefzayed@yahoo.com
Subject: Re: [Jalview-discuss] truncated image eps formatHi Muhammad
I am trying to export my msa with its structure prediction from jalview environment in eps format but the exported image is always truncated from its four sides. Is there any solution or suggestion? Many Thanks.Thanks for sending me your alignment. I performed a secondary structure prediction and tried to export the EPS and also saw that the figure was truncated. It is definitely a bug - https://issues.jalview.org/browse/JAL-2695
As a work around, I found that if you right click on the ‘reference sequence’ - the one you performed a secondary struture prediction on, and select ‘Hide Insertions’ - you can export an EPS containing the full secondary structure prediction without it being truncated.
We’ll take a look at this - thanks very much for emailing !
Jim.–
The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________ Jalview-discuss mailing list [Jalview-discuss@jalview.org](mailto:Jalview-discuss@jalview.org) [http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss)
The University of Dundee is a registered Scottish Charity, No: SC015096
···
On 07/09/2017 11:40, Mungo Carstairs (Staff) wrote:
On 21/08/2017 20:50, Jim Procter wrote:
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
--
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk)
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
The University of Dundee is registered Scottish charity: No.SC015096
Hi All,
Thank you so much for your detailed answer. yes, using hide insertions works good with me, while I would prefer to have such long sequence to be in multiple pages, but that is good at least I can show it. I do not have any expertise using ALSCRIPT software especially that it seems it does not have any GUI. So I would prefer hide insertions solution “Many thanks Jim for this suggestion”. However, I have a question about hide insertion tool, how it works ? cause it hide some big regions while leaving other gaps, how it decides it is an insertion ? Is this based only on the first sequence ? Does Jalview predict structure only excluding these insertions, if so what if there is an important functional alpha helix in these insertions ?!
Mmm. In principle, EPS should cope with anything, but as you have found, some viewers/software has limits on the total size of an image.
If this persists as a problem you might like to try the old ALSCRIPT software to make your eps files. This is more complex to use than Jalview, but will tile very large alignments over multiple EPS pages that you can then view or print separately. They are in one file though, so this may still be a problem for some software.
There is a link to the download page for ALSCRIPT here: http://www.compbio.dundee.ac.uk/software.html
You can generate the alignment format the ALSCRIPT needs from Jalview, it is blc or block file format.
Geoff.
···
On Thursday, 7 September 2017, 6:48, Geoff Barton gjbarton@dundee.ac.uk wrote:
On 07/09/2017 11:40, Mungo Carstairs (Staff) wrote:
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 when viewed in (Mac) Preview, but complete when viewed with Adobe Illustrator. Your alignment (2773 columns) generates an EPS image which is truncated when viewed in either Preview or Illustrator.
Hopefully Jim’s suggestion for a workaround can help you, otherwise I’m afraid this seems to be a limitation of the EPS output format.
…unless any other Jalview users with more knowledge of image handling software than me can chip in with suggestions!
Best regards,
Mungo
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK
www.jalview.org
www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017
From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Jim Procter jprocter@compbio.dundee.ac.uk
Sent: 28 August 2017 11:12:42
To: jalview-discuss@jalview.org; mhdatefzayed@yahoo.com
Subject: Re: [Jalview-discuss] truncated image eps formatHi Muhammad
On 21/08/2017 20:50, Jim Procter wrote:
On 21/08/2017 00:02, Muhammad Zayed wrote:I am trying to export my msa with its structure prediction from jalview environment in eps format but the exported image is always truncated from its four sides. Is there any solution or suggestion? Many Thanks.Thanks for sending me your alignment. I performed a secondary structure prediction and tried to export the EPS and also saw that the figure was truncated. It is definitely a bug - https://issues.jalview.org/browse/JAL-2695
As a work around, I found that if you right click on the ‘reference sequence’ - the one you performed a secondary struture prediction on, and select ‘Hide Insertions’ - you can export an EPS containing the full secondary structure prediction without it being truncated.
We’ll take a look at this - thanks very much for emailing !
Jim.–
------------------------------------------------------------------- Dr JB Procter, Jalview Coordinator, The Barton Group Division of Computational Biology, School of Life Sciences University of Dundee, Dundee DD1 5EH, UK. +44 1382 388734 | [www.jalview.org](http://www.jalview.org/) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk/)The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________ Jalview-discuss mailing list [Jalview-discuss@jalview.org](mailto:Jalview-discuss@jalview.org) [http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss)
--
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk)
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk/) | twitter: @gjbarton
The University of Dundee is registered Scottish charity: No.SC015096
The University of Dundee is a registered Scottish Charity, No: SC015096
Hi Muhammed - I suspect we lost your email from September in our spam folders once again. Really sorry about this!
Since my last e-mail, I did not not receive anything from Jalview-discuss as usual. I was wondering did I do any mistake that require me to be removed from the list ?! Does any of my questions were sent in an impolite way or went out of Jalview discussion policy. Many thanks !!
You’ve been perfectly polite - and incredibly patient 
Thank you so much for your detailed answer. yes, using hide insertions works good with me, while I would prefer to have such long sequence to be in multiple pages, but that is good at least I can show it. I do not have any expertise using ALSCRIPT software especially that it seems it does not have any GUI. So I would prefer hide insertions solution “Many thanks Jim for this suggestion”.
You are very welcome !
However, I have a question about hide insertion tool, how it works ? cause it hide some big regions while leaving other gaps, how it decides it is an insertion ?
Jalview examines the currently selected region, and hides columns that contains only gap characters. If you use the lates version of Jalview (2.10.2b2), you should be able to check that is the case in the Overview window.
Is this based only on the first sequence ?
Earlier versions of Jalview only used the first sequence - but in version 2.10.2 we changed it so it now looks at the current selection, or the sequence under the mouse if there is no selection.
Does Jalview predict structure only excluding these insertions,
Yes - Jalview’s structure prediction operates on just the visible alignment data, so by hiding columns you change the data that is used for prediction. However, JPred4 only looks at columns in the alignment where there is not a gap in the first sequence… so in fact, the prediction will be no different if you excluded gapped columns in Jalview before submitting the alignment for prediction. The most accurate predictions are made by submitting the sequence on its own to JPred4 - then, a sequence profile is calculated by running PSI-Blast.
if so what if there is an important functional alpha helix in these insertions ?!
This is the fundamental problem with sequence analysis - if the insertions are truly not homologous with your sequence of interest, then those functional regions are either absent in your sequence, or the function is being achieved in a different way (are there regions of your sequence of interest which are inserted with respect to the other genes ? sometimes the position of functional regions relative to other parts of the sequence can change, whilst the structural roles stay the same, but this is usually only for recent adaptations in distantly related organisms).
I hope this helps!
Jim.
···
On 22/10/2017 04:22, Muhammad Zayed wrote:
--
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)