[Jalview] Missing characters in alignment exported as EPS figure

Dear Haiwei.

Geoff Barton passed your email on to me, since I coordinate the Jalview project. Normally, I deal with emails like yours via the Jalview discussion list (which I've cc'ed this reply to), and I strongly recommend you join it. Registration is very easy - simply enter your email address in the web form here:

Regarding your email, it appears that the problem you experienced with your EPS file is due to an incorrect font substitution. When first opening the file, you probably saw some warning dialog boxes about this (something like 'font sans.italic not found, substituted with default'). You can do either of the following:

1. Export your alignment as EPS after first checking the 'lineart' option. This option is in the output tab of the preferences dialog box.

2. Change the font used to render the alignment before exporting - do this from the Font option in the 'Format' menu on the alignment window.

3. Install more fonts via the Adobe Font Manager, or modify the default font substitution settings in Illustrator. It may be that you are experiencing a unicode translation problem (where the alignment characters are being translated into a non-western typeface and so not appearing correctly).

Option 1 is recommended if you want to embed the artwork directly in a publication, since Jalview will render each character as shapes rather an as a text label. Option 2 is required if you want to modify the sequence labels or other text information on the figure using Illustrator.

Hope this helps!
Jim Procter.


On 06/10/2010 08:47, Geoff Barton wrote:

-------- Original Message --------
Subject: Jalview
Date: Tue, 5 Oct 2010 11:06:37 -0400
From: Haiwei Luo <hluo2006@gmail.com>
To: g.j.barton@dundee.ac.uk

Dear Dr. Barton,

I am trying to open my alignment and save it to EPS file (color coded)
using Jalview. When I open with adobe illustrator, the positions of many
amino acids are moved. Could you let me know a method to make it better,
or could you kindly produce an EPS file for me? I attached the alignment
and the EPS file.


Haiwei Luo
University of Georgia

J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.