[Chimera-users] 1 out of many helices shown as pipe

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 3 09:55:51 PST 2011

Hi Jason,
If you just want one or more cylinders showing helices, I suggest using the Axes/Planes/Centroids tool instead of PipesAndPlanks.  It allows for much more control over the individual objects.

First,  get rid of any existing pipes and planks:  open the Model Panel from the Favorites menu, close the model(s) created by PipesAndPlanks.

Start Axes/Planes/Centroids (under Tools... Structure Analysis in the menu), click "Define axes..."   If you just take the default settings, it will make a cylinder to show the axis of each helix in the structure, but you can hide them individually later:  the dialog will list the axes, and you can uncheck the "Shown" box for the ones you want to hide.  You can also click the square color wells to change their colors individually. 

Click the Help button or see here for details on axis creation and what you can do with the axes:

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 Mar 3, 2011, at 9:29 AM, odonnell at chem.fsu.edu wrote:

> Hi all,
> I have a pdb with many alpha helices but I only want one or two to  
> stand out as a pipe. I tried highlighting that particular sequence(s)  
> and going to Depiction => pipesAndPlanks but it will change all of them.
> Many thanks for a push in the right direction.
> -Jason

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