[Chimera-users] CAs not on ribbon

[Elaine Meng]

Hi Luyuan,
I'm glad the transparent ribbon raytracing has improved.

Now, to your questions:

(1) CA atoms not on ribbon.  This is because the ribbon is a smooth  
interpolation, so in some places it does not fall exactly on the  
backbone atoms.  There is no absolute fix currently, but some possible  
ways to make the figure look better are:

- show the CA atoms as larger balls so that it is less obvious that  
they are not on the ribbon.  Maybe you are showing "balls" (default  
0.25 of VDW radius) and could instead show "spheres" (equal to VDW  
radius).  If that is too big, you could still use the ball  
representation but change the model's "ball scale" factor to something  
larger than 0.25.  This can be done by selecting some part of the  
structure, opening the selection inspector (Actions... Inspect),  
inspecting  "Molecule model" and editing the "ball scale" factor.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ 
inspection.html#molprop>

- instead of showing ribbon, just show the CA atom trace as sticks and  
any specific CA atoms you want to highlight as balls or spheres. I  
agree this is not as pretty as the ribbon, however.

(2) ribbon too thick?  I'm not sure I understand this issue, but it  
sounds like you could just use the "flat" ribbon, which has no  
thickness (it does not use the height values).   You can switch to  
this ribbon style with the menu (Actions... Ribbon... flat) or with a  
command, e.g. ribrep flat
You can still change the widths in the Ribbon Style Editor as you  
prefer.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Dec 12, 2008, at 8:16 AM, lvyuan zhang wrote:

> Dear Chimera Team,
>       I tried yesterday's build and it worked nice for my purpose.  
> It totally solved the transparent ribbon problem that always bothers  
> me. Thank you so much!
>      Besides that, I still have two concerns.
>      1. When I show a Ca with both sphere and ribbon, these two do  
> not overlap well. The ribbon supposedly should go through the center  
> of the sphere, but it actually only goes through the edge of the  
> sphere. Can you please solve this?
>      2. In the ribbon style editor, the heights can not go below  
> 0.05. This becomes a problem when I raytrace a partially transparent  
> helix with low resolution. The image is obviously blurred, and the  
> blurness is caused by the slight shift between the two faces of the  
> helix. It looks better if I save image with high resolution, but you  
> know high resolution takes longer time.
>     Thank you again!
> Best
> Luyuan Zhang