[Jalview-discuss] Image export in EPS LineArt format on Mac does not work

Mungo Carstairs (Staff) g.m.carstairs at dundee.ac.uk
Thu Aug 23 09:00:34 BST 2018


Hello Petya,


Adjusting Jalview's memory settings is documented at http://www.jalview.org/jvmmemoryparams.html (linked from www.jalview.org<http://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




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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<http://www.jalview.org>

www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk>
g.m.carstairs at dundee.ac.uk<mailto:g.m.carstairs at dundee.ac.uk>



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From: Petya Violinova Krasteva <pvk2 at cornell.edu>
Sent: 23 August 2018 08:52:15
To: Jim Procter
Cc: Mungo Carstairs (Staff); jalview-discuss at jalview.org; petya.krasteva at 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 at compbio.dundee.ac.uk<mailto:jprocter at 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...


1) 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).


2) 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.)


3) Are you able to share the output EPS file (by private email if preferred)?


4) 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





[University of Dundee shield logo]<http://uod.ac.uk/sig-home>

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<http://www.jalview.org>

www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk>
g.m.carstairs at dundee.ac.uk<mailto:g.m.carstairs at dundee.ac.uk>



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We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline>
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From: jalview-discuss-bounces at jalview.org<mailto:jalview-discuss-bounces at jalview.org> <jalview-discuss-bounces at jalview.org><mailto:jalview-discuss-bounces at jalview.org> on behalf of Petya Violinova Krasteva <pvk2 at cornell.edu><mailto:pvk2 at cornell.edu>
Sent: 10 August 2018 15:02:28
To: jalview-discuss at jalview.org<mailto:jalview-discuss at 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 at cornell.edu<mailto:pvk2 at cornell.edu>
petya.krasteva at i2bc.paris-saclay.fr<mailto:petya.krasteva at i2bc.paris-saclay.fr>


The University of Dundee is a registered Scottish Charity, No: SC015096


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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
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--
__________________________________________________

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 at cornell.edu<mailto:pvk2 at cornell.edu>
petya.krasteva at i2bc.paris-saclay.fr<mailto:petya.krasteva at i2bc.paris-saclay.fr>



The University of Dundee is a registered Scottish Charity, No: SC015096
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