Missing aligned sequences in image!

I am trying to export my sequence alignment (made in clustalW)after making really pretty pictures for publication. However I cannot get the whole alignment in the .eps image file (or in .png file) and it is missing a block of alignment.I tried to have minimum characters in the header of the fasta sequences (before running clustalW),I tried decreasing the font size, I tried changing it from portrait to landscape but to no effect.I wrap everything,get rid of the annotations but nothing works.Its always a one page .eps image with the top-alignmnet-block of first ~50 residues missing everytime.
I really like the figures I made in jalview, but I am really frustrated as I need the whole alignment for publication.

I have a multiple sequence alignment of 11 sequences each of 300 residues.
It would be of immense help if I could get the whole alignment, so that I could put it in the publication.


Subhendu Chakraborti
Graduate student
Bahnson's Group (Structural Enzymology)
Department of Chemistry & Biochemistry
312 Drake Hall, University of Delaware
Newark, DE 19716 USA


subhendu@UDel.Edu wrote:

Hi Jim,
Sending the jalview project (subhendu.jar)and a couple of .eps file.Please notice the change when I change the font size.

Received correctly. I checked with the current 2.4 version of jalview
and the project file is fine. It also seems to export correctly when I
try png and eps for myself. This means it isn't a bug in Jalview - which
is good news for you!

When I looked at your EPS files in Adobe Illustrator, I noticed that the
first block is usually outside the page bounding box. I'm not sure what
you are using to view the EPS files, but I suspect that it is not
computing the artwork bounding box correctly - and so clipping off the
first block of alignment (and in the font size 8 case, cutting off the
top 8 sequences of the first block.

If you can't get access to a program like Illustrator, another trick is
to use something like ghostscript + gsviewer - which are available for
free - they will let you scale and view the eps file. you can also used
distiller to translate the eps into a pdf file - but you have to make
sure the print settings are set so distiller scales the artwork to the page.

let me know if you have any more problems - I'll ask my colleagues if
they know of any free/cheap postscript lineart editors (Xara is one, and
corel draw would also do fine).



J. B. Procter (ENFIN/VAMSAS) 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.