Hi Frank,
No problem for the question - it is always nice to hear from people who use the tools we develop.
In general, the best way to save for publication is an EPS since this is vector graphics and so independent of resolution. You should not get low resolution with EPS output, so I'm not sure how you are getting low resolution with EPS. It may be that you are importing the EPS into some other program that then renders it at low resolution. An EPS will scale to any size without loss of quality.
So, ideally send the EPS file that is output from Jalview to the journal. Most journals will take this format for figures.
If the journal insist on a PNG or JPG, then the best solution is to Export first as EPS (File->Export Image->EPS) and then open in Adobe Illustrator. You can then use illustrator to export as a PNG or JPG at whatever size/resolution you like. You can also use Illustrator to add extra annotations to your figure. If you don't have illustrator there are a few other programs that will handle EPS format and allow you to edit it and export it. e.g. Inkskape which works quite nicely.
I hope this helps.
All the best,
Geoff.
P.S. Incidentally, I recommend you sign up to the jalview-discuss mailing list and post questions like this there. The mailing list will reach a lot of jalview users as well as us and you may sometimes get a quicker response to a question. You can sign up on the Jalview website. For now, I have copied this message to the list so that others can see my answer.
ยทยทยท
On 05/03/2014 03:20, Frank Eisenhaber wrote:
Dear Geoffrey,
Sorry for enlarging your mailbox with yet another message. To note, we
produced publication images of alignments always with your JalView tool
over the last couple of years. Yesterday, we were told by a journal that
they wish to have the images with 300 px/in when the output of JalView
regardless of PNG or EPS is 72 px/in. Is there a way to achieve that?
With kind regards, Frank.
--
Geoff Barton Professor of Bioinformatics
Head of Division of Computational Biology College of Life Sciences
University of Dundee, Scotland, UK. g.j.barton@dundee.ac.uk
Tel:+44 1382 385860 www.compbio.dundee.ac.uk
The University of Dundee is registered Scottish charity: No.SC015096