[Chimera-users] post-processing of Chimera images

Jonathan Hilmer jkhilmer at gmail.com
Mon Apr 28 13:10:07 PDT 2008


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:

Here are some of the screenshots:

I've got an example figure that you can see that uses some of the
basic features with images, shapes, figures, and text:

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.


On Mon, Apr 28, 2008 at 1:00 PM,  <chimera-users-request at 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)
>  ----------------------------------------------------------------------
>  Message: 1
>  Date: Mon, 28 Apr 2008 09:07:02 -0700
>  From: Jeff Speir <speir at scripps.edu>
>  Subject: Re: [Chimera-users] Numbering the amino acid sequence
>  To: chiendarret at yahoo.com
>  Cc: chimera <chimera-users at cgl.ucsf.edu>
>  Message-ID: <B2AD9487-6EEF-4AC4-8060-51788F8E86B2 at 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

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