Francesco: Especially since you're preparing images for publication, I would recommend you use software such as Inkscape (a excellent free alternative to Adobe Illustrator) to handle the composition of figures. It's a vector-based program that's much better suited to handling geometric shapes as compared to a raster program like Photoshop or Gimp. The final post in the following discussion has a good overview with screenshots showing how Inkscape can be used: http://inkscape-forum.andreas-s.net/topic/146897 Here are some of the screenshots: http://jo.irisson.free.fr/dropbox/inkscape/poster_inkscape_style2.png http://jo.irisson.free.fr/dropbox/inkscape/poster_inkscape_outline.png I've got an example figure that you can see that uses some of the basic features with images, shapes, figures, and text: ftp://guest:@bothnerlab01.chemistry.montana.edu/inkscape_example.zip The best part of using Inkscape is that it's totally resolution-independent, so you can export graphics for publication at whatever resolution or format is required. There are only two disadvantages to Inkscape that I have found so far. First, the PDF export option works fine but treats text as shapes, so the resulting files are huge if there is substantial amounts of text: ~500MB for a poster with about 50% text. Second, it doesn't embed images within the saved files the way Powerpoint does: it just saves links in the manner of OpenOffice. I rather prefer that behavior, but you have to be prepared for it if you're moving files around. Regardless, once you give it a try you'll never go back to using Powerpoint or Photoshop for making figures or posters. Jonathan On Mon, Apr 28, 2008 at 1:00 PM, <chimera-users-request@cgl.ucsf.edu> wrote:

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Today's Topics:

1. Re: Numbering the amino acid sequence (Jeff Speir) 2. Re: Chimera - Matchmaker tool (Elaine Meng) 3. Re: Numbering the amino acid sequence (Eric Pettersen)

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Message: 1 Date: Mon, 28 Apr 2008 09:07:02 -0700 From: Jeff Speir <speir@scripps.edu> Subject: Re: [Chimera-users] Numbering the amino acid sequence To: chiendarret@yahoo.com Cc: chimera <chimera-users@cgl.ucsf.edu> Message-ID: <B2AD9487-6EEF-4AC4-8060-51788F8E86B2@scripps.edu> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

Outside of Chimera, there are several ways to do this in image editing programs (Gimp, Photoshop, etc.). Use layers and: 1) draw arrows; or 2) place the number on top of a box just big enough to fit the text (opaque to semi-transparent); or 3) use effects on the text, such as adding an outer glow effect in Photoshop, which adds a halo around the text so that its outline stands out from the image, making it readable.

I would advise not going crazy with colors, this just adds to the complexity of the image.

Cheers,

Jeff

On Apr 27, 2008, at 10:49 AM, Francesco Pietra wrote:

...

A referee is asking me to number the amino acid sequence involved in docking a ligand with a protein. Not satisfied by having a side table with a guideline.

Is it possible to add that numbering in a least-intruding way? The figure exported in standard graphic formats from Chimera is already extremely crowded. Therefore, is any possibility of adding the numbering outside the protein with some kind of pointers? I can't do with colors alone: I already used different colors for different helices.

Thanks francesco pietra