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

Jim Procter jprocter at compbio.dundee.ac.uk
Wed Aug 22 11:31:24 BST 2018


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
>
>
>
> Email signature
>  
> 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>
>
>
> University of Dundee Facebook <http://uod.ac.uk/sig-fb> University of
> Dundee Twitter <http://uod.ac.uk/sig-tw> University of Dundee LinkedIn
> <http://uod.ac.uk/sig-li> University of Dundee YouTube
> <http://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
>
> ------------------------------------------------------------------------
> *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
>  
> 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
>
>
> _______________________________________________
> Jalview-discuss mailing list
> Jalview-discuss at jalview.org
> 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 | www.compbio.dundee.ac.uk

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20180822/1c3f0f3e/attachment-0001.html 


More information about the Jalview-discuss mailing list