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

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 6 14:22:49 PDT 2011

Hi Keren,
There is no arrow in PipesAndPlanks -- for that you could show the strands as regular ribbons.  You can show ribbon for just the strands (no ribbon for helix or coil) -- the "edged" style is more boxlike -- and adjust ribbon dimensions such as thickness using Ribbon Style Editor (under Tools... Depiction in the menu).

You could try to combine pipes from PipeAndPlanks with ribbon representations of the strands.  It might be possible by making the planks thin enough to be hidden inside the ribbon, but I have not tried this specifically, so don't know for certain that it would work.  Another possible trick is to put the helices and strands into separate PDB input files, and use PipesAndPlanks on one and ribbons on the other, but I haven't tried that either.

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 Sep 6, 2011, at 11:58 AM, Keren Lasker wrote:

> 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
>> 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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