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

Mungo Carstairs (Staff) g.m.carstairs at dundee.ac.uk
Fri Aug 10 17:08:19 BST 2018

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,


[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


g.m.carstairs at dundee.ac.uk<mailto:g.m.carstairs at dundee.ac.uk>

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From: jalview-discuss-bounces at jalview.org <jalview-discuss-bounces at jalview.org> on behalf of Petya Violinova Krasteva <pvk2 at cornell.edu>
Sent: 10 August 2018 15:02:28
To: jalview-discuss at jalview.org
Subject: [Jalview-discuss] Image export in EPS LineArt format on Mac does not work


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 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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