[chimerax-users] Showing long coiled coil alpha helices as tubes

[Tom Goddard]

Hi Juha,

The curved cylinders that ChimeraX makes for alpha helices have a cylinder axis that is the arc of a circle.  They cannot twist like a helix.  The cylinder axis arc always lies in a plane.  The code optimizes the curved cylinder to put the C-alpha atoms as close to the surface of the cylinder as possible.

While you could try to define your own center line for the "shape tube" command by placing markers along the center of the spiralling alpha helices it will probably be difficult to get a smooth appearance.

	Tom

> On Dec 13, 2021, at 8:57 AM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Juha,
> I believe that for a single helix, the tube algorithm either makes a single smooth arc or a straight tube, rather than putting multiple different arcs together... so it is true that it may not follow the path of the helix very well, especially long ones that curve differently or in different directions along their lengths.  I don't know if there is something that can be tweaked by changing the code -- somebody else would need to advise on that.
> 
> From the noncoding perspective, I don't have any great alternatives:
> (A) use the regular non-tube ribbon representation of helices, or 
> (B) keep using tubes but maybe breaking the helix up into multiple helices by changing the ss_id attribute, e.g. as mentioned here
> <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-October/000687.html>
> 
> There is a "shape tube" command, but given the CAs it will still make a spiral rather than first determining a central helix axis and then making a tube around it.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html#tube>
> 
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Dec 13, 2021, at 12:05 AM, Huiskonen, Juha T via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Hi all, 
>> I am trying to render two long alpha helices forming a coiled coil as tubes instead of ribbons. 
>> The tubes rendered with default settings do not however follow the paths of the helices. Instead, the tubes become almost straight. Any suggestions? 
>> Best wishes,
>> Juha 
> 
> 
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