[Chimera-users] post-processing of Chimera images
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:
> Send Chimera-users mailing list submissions to
> chimera-users at cgl.ucsf.edu
> To subscribe or unsubscribe via the World Wide Web, visit
> or, via email, send a message with subject or body 'help' to
> chimera-users-request at cgl.ucsf.edu
> You can reach the person managing the list at
> chimera-users-owner at cgl.ucsf.edu
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Chimera-users digest..."
> 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.
> 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
More information about the Chimera-users