[Chimera-users] show alpha-carbon as sphere in chimera

[Elaine Meng]

On Mar 18, 2013, at 8:07 PM, Feixia wrote:

> Hi Elaine,
> Is there a way to show alpha-carbon only in Chimera as sphere?  I can show beta-carbon, but always together with alpha-carbon.  Alpha-carbon for some reason doesn't show by itself.  Thanks a lot.
> Best,
> Feixia

Hi Feixia,
Maybe you are also displaying ribbon.  By default when the ribbon is shown, the alpha-carbon will not show.  You can allow showing both ribbon and alpha-carbon with command: 
ribbackbone  
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html>

However, you can see the "real" position of the alpha-carbon is not exactly on the ribbon.  Sometimes it will seem to float away, and the image might not look good.  That is because the default ribbon is a smooth interpolation.

Possible ways to handle this issue:

(a) don't show ribbon

(b) make the alpha-carbon sphere(s) big enough and/or change the viewing angle so it is not obviously floating away from the ribbon.  Whether this is possible depends on which positions you are displaying and the specific backbone conformation in those areas.

(c) change the ribbon from the default B-spline to cardinal spline, with or without some compromise smoothing, for example with commands:
ribspline cardinal
ribspline cardinal smooth strand
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html>

More discussion/explanation of this issue:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset>

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