[Chimera-users] solid-cylinder representation of helices

[Elaine Meng]

Hi Francesco,
There are at least two ways to show helices as cylinders in Chimera:  

(A) PipesAndPlanks (under Tools... Depiction), which also shows beta-strands as rectangular boxes or "planks"
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pipesandplanks/pipesandplanks.html>

(B) Axes/Planes/Centroids (under Tools... Structure Analysis), in which axes are shown as cylinders.  You can use any set of atoms to define an axis, but one of the options is to make one for each helix. 
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>

Method (B) allows you to change cylinder colors individually after they have been created (using the square color wells) and to make measurements involving the axes.  Both methods allow you to specify the cylinder radius or have it figured out automatically.  

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

On May 19, 2011, at 8:04 AM, Francesco Pietra wrote:

> HI:
> Is any plan about a solid-cylinder representation of protein helices?
> It would be very useful to represent pathways of ligands inside a
> protein (in combination with centroid). Helices allow a less defined
> 3D perspective, especially when all is projected into a screen or
> paper.
> Thanks
> francesco pietra