[Chimera-users] Numbering the amino acid sequence

Jeff Speir speir at scripps.edu
Mon Apr 28 09:07:02 PDT 2008

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
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