[Chimera-users] is there a way to draw a small loop as broken line?

[jinghua at ucsd.edu]

hi Elaine,

   Thank you for your advice! I tried a clumsy way to select every other
   residue and change its color. Some one might have more elegant ways.

   Best wishes,

   Jinghua

On Wed, 16 Dec 2009, Elaine Meng wrote:

> Hi Jinghua,
> I don't know any way to make the smooth ribbon "broken."  You can draw a 
> straight line between any pair of atoms (with Pseudobond Reader or by 
> creating a distance measurement) and control how that line is drawn (solid, 
> dashed, etc.), but if you wanted a curved dashed line, you would have to add 
> that with some other program like Photoshop after saving the image.
>
> You might try making the ribbon for one of the conformations transparent, as 
> shown in the image here:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html>
>
> Example command:
> color 0.8,0,0.4,0.4,r #0:20-48.b
>
> where the color is defined with red,green,blue,opacity numbers and the ",r" 
> means ribbons only for residues 20-48 in chain B of model 0.
>
> 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 Dec 15, 2009, at 7:38 PM, jinghua at ucsd.edu wrote:
>
>>
>>  To differentiate two conformations of a small loop, does anyone know
>>  how to draw one of the loop (a smooth C alpha trace) as broken line?
>>
>>  Thank you for your kind help!
>>
>>  Jinghua
>> 
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