[Chimera-users] depicting secondary structure elements

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 16 13:43:13 PDT 2012

Hi Jordi,
Funny you should ask, there is a "PipesAndPlanks" tool that has been undergoing significant improvements over the last few days.  This tool exists in older versions, but I would recommend getting the newest daily build if you want to try it (menu Tools... Depiction.. Pipes and Planks).  This tool shows helices as cylinders, strands as rectangular boxes, and the remaining "coil" as connectors between them. 

Alternatively, Axes/Planes/Centroids (under menu Tools... Structure Analysis) allows creating cylindrical axes from any sets of atoms, such as each protein helix.  Whereas "pipes and planks" are for illustration purposes, these axes are also useful in distance/angle measurements; conversely, however, they are not connected to anything else.

In the March 16 daily build, PipesAndPlanks has problems with 2-residue secondary structure elements and MSE residues. These problems have been fixed and the fixes will be available in the *next* successful daily build.

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 16, 2012, at 12:06 PM, Jordi Querol Audi wrote:

> Dear Chimera developers,
> I would like to show a fitting of a pdb into my EM reconstruction but instead of displaying helices and b-sheets I would prefer to use cylinders or tubes. Is there any way to display a pdb this way?
> Thank you so much in advance,
> Jordi

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