[Chimera-users] Drawing a circle or square

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 30 12:32:56 PDT 2008

Hi Pradeep,
Other people have recommended Adobe Illustrator and Inkscape for such  

However, you CAN draw a rectangle in the BILD format and read that  
into Chimera.  For example, put the following 7 lines in a text file  
named square.bild and open it with File... Open:
.scale 1.5
.color red
.move 0 0 0
.draw 5 0 0
.draw 5 5 0
.draw 0 5 0
.draw 0 0 0

I also attach said file below, for your convenience.  You can edit  
the coordinates, scale, and color.  Once you open it in Chimera, it  
is a separate model, and you can move it independently using the  
checkboxes below the Command Line or the "Active" checkboxes in the  
Model Panel.  Advantage: since it does exist in 3D, you can place it  
between the surface and the nucleic acid.  Disadvantage: cannot make  
curves/circles, may be hard to position/orient, cannot control line  
thickness.  The thickness issue may be addressed by instead making  
the edges cylinders and the corners balls.  This can also be done in  
the simple BILD format, but it is sort of a hack to make a 3D object  
when you really want a 2D object.

BILD format description:

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 30, 2008, at 11:57 AM, Pallan, Pradeep S wrote:

> Hi Elaine,
> I am wondering whether one can draw a circle or a square
> to indicate a site/s of a protein? Attached is a tiff file that has a
> square and a circle. I want the regions to be pointed out.
> So what I did:
> 1) Generated the image in chimera
> 2) added a circle and a square in microsoft paint (Doesn't look  
> good!).
> I was going through the chimera tutorials, but didn't find the  
> feature.
> Any suggestions for adding a circle or square? In my case, the
> surface image is at the back, and nucleic acid in the front.
> I would like to draw the circle and square and then load the nucleic
> acids, so that will look better. In other words the square or  
> circle in
> between
> the surface image (at the back) and the nucleic acid (in front).
> If editing the tiff file using Adobe photoshop (instead of MS paint)
> it does a better job, thick lines etc, but it leaves patches on the  
> nucleic
> acid.
> I appreciate your help.
> Thanks,
> Pradeep

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