[Chimera-users] depicting secondary structure elements

Jordi Querol-Audi jquerolaudi at gmail.com
Tue Mar 20 08:50:28 PDT 2012

Hi Elaine,
thank you so much for your help.


On Fri, Mar 16, 2012 at 9:43 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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.
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pipesandplanks/pipesandplanks.html
> >
> 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.
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes
> >
> 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.
> <http://www.cgl.ucsf.edu/chimera/download.html#daily>
> 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 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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