[Chimera-users] structure analysis -> axes/planes/centroids

Keren Lasker kerenl at salilab.org
Tue Sep 6 11:58:41 PDT 2011

Thanks Elaine.
Just one quick question is there an option to add arrows to the planks ? 
On Sep 6, 2011, at 9:40 AM, Elaine Meng wrote:

> Hi Keren,
> There is no option to show in a single step an axis cylinder for each strand in a structure, but you could do it one strand at a time.  For example, command:
> define axis :/ssId=1 & strand & @n,ca,c
> to use the backbone atoms N,CA,C of the first strand in the structure.  
> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
> Or you could select the atoms, e.g. for the second strand
> select :ssId=2 & strand & @n,ca,c
> then use the Define Axes GUI with the selected atoms option.
> However, it is unusual to use cylinders to represent strands.  There is a different tool, PipesAndPlanks (under Tools... Depiction in the menu) that in one step shows all the helices as cylinders or "pipes" and all the strands as rectangular boxes or "planks".  However, that tool has less flexibility in coloring - all the planks would be the same color as each other, for example.
> <http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pipesandplanks/pipesandplanks.html>
> 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 Sep 6, 2011, at 5:23 AM, Keren Lasker wrote:
>> Dear Chimera group:
>> I have a quick question regarding low resolution representation of secondary structures.
>> In the structure analysis -> axes/planes/centeroids tool there is an option of representing each helix as a axis.
>> Is there a similar option for representing strands?
>> thanks, Keren.

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