Hello,
I am trying to export some alignment images from Jalview into high-resolution EPS format for downstream figure making in photoshop. I am working on a MacAir with MacOS High Sierra. While this functionality was working fine a few weeks ago, it no longer does as I am getting black insets for the alignment part of the image and only the text for the sequences’ titles on the left is visible in the exported .eps file. I am not sure why this problem appeared. I tried to update both Jalview and my Mac, but the problem persists. Any ideas why this occurs and how it can be fixed?
Thanks in advance,
Petya
···
Petya V. Krasteva, Ph.D.
Group Leader ‘Structural Biology of Biofilms’
Department of Biochemistry, Biophysics and Structural Biology
Institute for Integrative Biology of the Cell (I2BC)
91190 Gif-sur-Yvette, FR
pvk2@cornell.edu
petya.krasteva@i2bc.paris-saclay.fr
Hello Petya,
Sorry to hear that! To help me investigate…
-
Can you confirm the versions of Jalview and Java that you are running - this is logged at the start of the Jalview Console output (Tools | Show Java Console).
-
Do you choose ‘Text’ or ‘Lineart’ for the EPS output?
(If you don’t see this option, you may have it set as a preference EPS_RENDERING in your home directory .jalview_properties file.)
-
Are you able to share the output EPS file (by private email if preferred)?
-
Does this also happen with our ‘example’ alignment? To load this:
File | Input Alignment | From URL…| http://www.jalview.org/examples/uniref50.fa
Thanks and 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 Petya Violinova Krasteva pvk2@cornell.edu
Sent: 10 August 2018 15:02:28
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Image export in EPS LineArt format on Mac does not work
Hello,
I am trying to export some alignment images from Jalview into high-resolution EPS format for downstream figure making in photoshop. I am working on a MacAir with MacOS High Sierra. While this functionality was working fine a few weeks ago, it no longer does as I am getting black insets for the alignment part of the image and only the text for the sequences’ titles on the left is visible in the exported .eps file. I am not sure why this problem appeared. I tried to update both Jalview and my Mac, but the problem persists. Any ideas why this occurs and how it can be fixed?
Thanks in advance,
Petya
Petya V. Krasteva, Ph.D.
Group Leader ‘Structural Biology of Biofilms’
Department of Biochemistry, Biophysics and Structural Biology
Institute for Integrative Biology of the Cell (I2BC)
91190 Gif-sur-Yvette, FR
pvk2@cornell.edu
petya.krasteva@i2bc.paris-saclay.fr
The University of Dundee is a registered Scottish Charity, No: SC015096
Dear Petya - I’m just following up on Mungo’s email.
The black insets you see are due to a bug in Jalview 2.10.4 (and 2.10.4b1) which only occur when a sequence is selected in the alignment view being exported as EPS (see https://issues.jalview.org/browse/JAL-3003).
We’re working on a fix for this, but for now, the simplest route is to simply press ‘Escape’ or use the Select->Deselect All menu item to clear the current selection before exporting as EPS.
Let us know if you have any problems!
Regards,
Jim Procter.
···
On 10/08/2018 17:08, Mungo Carstairs (Staff) 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)
Dear Jim, dear Mungo,
Thank you both for your e-mails. Indeed, I am now able to export the alignments properly for figures. It seems to also depend on the memory usage rigt before the export; what would be an easy way to increase the dedicated max memory? Also, is there a way to convert the coloring by PID to a different color scheme, such as the cyan-maroon one that is typically used for plotting surface conservation.
Thank you in advance if you would be able to reply.
Best,
Petya
···
On Wednesday, August 22, 2018, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:
Dear Petya - I’m just following up on Mungo’s email.
The black insets you see are due to a bug in Jalview 2.10.4 (and 2.10.4b1) which only occur when a sequence is selected in the alignment view being exported as EPS (see https://issues.jalview.org/browse/JAL-3003).
We’re working on a fix for this, but for now, the simplest route is to simply press ‘Escape’ or use the Select->Deselect All menu item to clear the current selection before exporting as EPS.
Let us know if you have any problems!
Regards,
Jim Procter.
On 10/08/2018 17:08, Mungo Carstairs (Staff) wrote:
Hello Petya,
Sorry to hear that! To help me investigate…
-
Can you confirm the versions of Jalview and Java that you are running - this is logged at the start of the Jalview Console output (Tools | Show Java Console).
-
Do you choose ‘Text’ or ‘Lineart’ for the EPS output?
(If you don’t see this option, you may have it set as a preference EPS_RENDERING in your home directory .jalview_properties file.)
-
Are you able to share the output EPS file (by private email if preferred)?
-
Does this also happen with our ‘example’ alignment? To load this:
File | Input Alignment | From URL…| http://www.jalview.org/examples/uniref50.fa
Thanks and 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 Petya Violinova Krasteva pvk2@cornell.edu
Sent: 10 August 2018 15:02:28
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Image export in EPS LineArt format on Mac does not work
Hello,
I am trying to export some alignment images from Jalview into high-resolution EPS format for downstream figure making in photoshop. I am working on a MacAir with MacOS High Sierra. While this functionality was working fine a few weeks ago, it no longer does as I am getting black insets for the alignment part of the image and only the text for the sequences’ titles on the left is visible in the exported .eps file. I am not sure why this problem appeared. I tried to update both Jalview and my Mac, but the problem persists. Any ideas why this occurs and how it can be fixed?
Thanks in advance,
Petya
Petya V. Krasteva, Ph.D.
Group Leader ‘Structural Biology of Biofilms’
Department of Biochemistry, Biophysics and Structural Biology
Institute for Integrative Biology of the Cell (I2BC)
91190 Gif-sur-Yvette, FR
pvk2@cornell.edu
petya.krasteva@i2bc.paris-saclay.fr
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)
--
-------------------------------------------------------------------
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)
–
Petya V. Krasteva, Ph.D.
Group Leader ‘Structural Biology of Biofilms’
Department of Biochemistry, Biophysics and Structural Biology
Institute for Integrative Biology of the Cell (I2BC)
91190 Gif-sur-Yvette, FR
pvk2@cornell.edu
petya.krasteva@i2bc.paris-saclay.fr
Hello Petya,
Adjusting Jalview’s memory settings is documented at http://www.jalview.org/jvmmemoryparams.html (linked from www.jalview.org - Documentation - FAQ).
I’m afraid the PID colours are currently fixed in Jalview. We could raise a feature request to provide the ability to change them if you think that would be useful.
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: Petya Violinova Krasteva pvk2@cornell.edu
Sent: 23 August 2018 08:52:15
To: Jim Procter
Cc: Mungo Carstairs (Staff); jalview-discuss@jalview.org; petya.krasteva@i2bc.paris-saclay.fr
Subject: Re: Image export in EPS LineArt format on Mac does not work
Dear Jim, dear Mungo,
Thank you both for your e-mails. Indeed, I am now able to export the alignments properly for figures. It seems to also depend on the memory usage rigt before the export; what would be an easy way to increase the dedicated max memory? Also, is there a way to convert the coloring by PID to a different color scheme, such as the cyan-maroon one that is typically used for plotting surface conservation.
Thank you in advance if you would be able to reply.
Best,
Petya
On Wednesday, August 22, 2018, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:
Dear Petya - I’m just following up on Mungo’s email.
The black insets you see are due to a bug in Jalview 2.10.4 (and 2.10.4b1) which only occur when a sequence is selected in the alignment view being exported as EPS (see https://issues.jalview.org/browse/JAL-3003).
We’re working on a fix for this, but for now, the simplest route is to simply press ‘Escape’ or use the Select->Deselect All menu item to clear the current selection before exporting as EPS.
Let us know if you have any problems!
Regards,
Jim Procter.
On 10/08/2018 17:08, Mungo Carstairs (Staff) wrote:
Hello Petya,
Sorry to hear that! To help me investigate…
-
Can you confirm the versions of Jalview and Java that you are running - this is logged at the start of the Jalview Console output (Tools | Show Java Console).
-
Do you choose ‘Text’ or ‘Lineart’ for the EPS output?
(If you don’t see this option, you may have it set as a preference EPS_RENDERING in your home directory .jalview_properties file.)
-
Are you able to share the output EPS file (by private email if preferred)?
-
Does this also happen with our ‘example’ alignment? To load this:
File | Input Alignment | From URL…| http://www.jalview.org/examples/uniref50.fa
Thanks and 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 Petya Violinova Krasteva pvk2@cornell.edu
Sent: 10 August 2018 15:02:28
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Image export in EPS LineArt format on Mac does not work
Hello,
I am trying to export some alignment images from Jalview into high-resolution EPS format for downstream figure making in photoshop. I am working on a MacAir with MacOS High Sierra. While this functionality was working fine a few weeks ago, it no longer does as I am getting black insets for the alignment part of the image and only the text for the sequences’ titles on the left is visible in the exported .eps file. I am not sure why this problem appeared. I tried to update both Jalview and my Mac, but the problem persists. Any ideas why this occurs and how it can be fixed?
Thanks in advance,
Petya
Petya V. Krasteva, Ph.D.
Group Leader ‘Structural Biology of Biofilms’
Department of Biochemistry, Biophysics and Structural Biology
Institute for Integrative Biology of the Cell (I2BC)
91190 Gif-sur-Yvette, FR
pvk2@cornell.edu
petya.krasteva@i2bc.paris-saclay.fr
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)
--
-------------------------------------------------------------------
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)
–
Petya V. Krasteva, Ph.D.
Group Leader ‘Structural Biology of Biofilms’
Department of Biochemistry, Biophysics and Structural Biology
Institute for Integrative Biology of the Cell (I2BC)
91190 Gif-sur-Yvette, FR
pvk2@cornell.edu
petya.krasteva@i2bc.paris-saclay.fr
The University of Dundee is a registered Scottish Charity, No: SC015096