[Chimera-users] DNA nucleotide bases representation as long sticks

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 23 10:39:21 PDT 2014

Dear Alexandra,
The Nucleotides tool has several display options, including “ladder” — this is similar to what is shown in the image, but not exactly the same because in Chimera, the “rungs” representing base pairs go all the way across instead of having a break in the middle.  There can be half-rungs where the base is not paired, but usually most are paired. 

One way to start this tool is with menu: Actions… Atoms/Bonds… nucleotide objects… settings.  (All its features are also available as numerous options of the “nucleotides” command.)  Use “Help” button on nucleotides dialog or command “help nucleotides” to see detailed documentation.

For ladder:
Show side (sugar/base) as “ladder”, see also sub-options lower in the dialog.  Example image attached below.

If you really did want breaks in the middle, you could try:
Show side (sugar/base) as “tube/slab”, Show base orientation “false”, and in the slab options: slab object “tube”.
Then in the slab style tab, you can change the rectangle dimensions to be skinny and tubelike.  For example, I set the upper right to “0.5” for both purine and pyrimidines.  However, this will give a doglegged tube (angle between sugar and based segments) rather than a single straight tube.  Example image attached below.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 23, 2014, at 3:14 AM, roz orchidea <roz.orchidea at gmail.com> wrote:

> Dear all,
> I am trying to make nice DNA images with Chimera. I would like to have my nucleotide bases shown as long sticks like in this image: http://www.nature.com/cr/journal/v23/n2/images/cr2012170f1.jpg 
> Does anybody know how to do that?
> Thanks in advance for you answer!
> Alexandra

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