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

Petya Violinova Krasteva pvk2 at cornell.edu
Thu Aug 23 08:52:15 BST 2018


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>
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
>
>
>
> [image: Email signature]
>
> [image: 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
>
> www.compbio.dundee.ac.uk
> g.m.carstairs at dundee.ac.uk
>
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> ------------------------------
> *From:* jalview-discuss-bounces at jalview.org <jalview-discuss-bounces@
> jalview.org> <jalview-discuss-bounces at jalview.org> on behalf of Petya
> Violinova Krasteva <pvk2 at cornell.edu> <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
> petya.krasteva at i2bc.paris-saclay.fr
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> _______________________________________________
> Jalview-discuss mailing listJalview-discuss at jalview.orghttp://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
>
>

-- 
__________________________________________________

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
petya.krasteva at i2bc.paris-saclay.fr
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