[Chimera-users] Numbering the amino acid sequence

Eric Pettersen pett at cgl.ucsf.edu
Mon Apr 28 10:36:23 PDT 2008

Also, the 2D Labels tool in Chimera (under Utilities) can place  
labels at arbitrary positions on the screen.  However it doesn't have  
the capability of drawing arrows yet, so if that is crucial to the  
understandability of the image you will have to make use of Jeff's  
excellent suggestions instead.


On Apr 28, 2008, at 9:07 AM, Jeff Speir wrote:

> 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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