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

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 8 12:55:12 PDT 2011

Hi Keren,
Just a little more follow-up.  I tried a couple of things to show helix cylinders with strand ribbons (arrows), but neither were very successful.  The problem in combining the different representation types is that they don't connect up well to each other.

I tried showing helices as either axes cylinders or Pipes (hiding planks and coil by setting their thickness and width to zero) + ribbons for everything else, for example commands: ribbon; ~ribbon helix

I tried showing helices and coils with PipesAndPlanks (hiding planks by setting their dimensions to zero) + ribbons for strands, for example command: ribbon strand

In both cases the different representation types didn't join up well.  In some places there were gaps and in others, the angle of connection was weird.  Sorry, there isn't a really good solution for showing helices as cylinders together with strands as arrows, since the arrow representation is only available in ribbons, not PipesAndPlanks.


On Sep 6, 2011, at 2:22 PM, Elaine Meng wrote:

> 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).
> <http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html>
> 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
> 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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