[Chimera-users] command related to the alignment of the ribbon form and the ball & stick form

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 24 09:33:09 PDT 2015


Dear Smith,
The default ribbon path is smoothed, which gives a nicer-looking ribbon but doesn't exactly match the positions of the backbone atoms.  I'm guessing this is what you meant.  

You can make the ribbon go exactly through the CA atom positions by using cardinal spline instead of the default B-spline, for example with command:

ribspline card

…as you can see, that gives a very wavy ribbon.  There are several command options for adjusting the parameters.  For example, I like to apply some compromise smoothing to just the beta-strands:

ribspline card smooth strand

See the manual page for explanations of the command options:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html>

To go back to the default ribbon path, command:

ribspline b

Further details:
<http://www.rbvi.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

On Mar 23, 2015, at 11:47 PM, "Smith Liu" <smith_liu123 at 163.com> wrote:

> Dear All,
>  
> If by Chimera we open a PDB and a corresponding mrc file, and we display the molecule by both ribbon format and ball & stick format, we can find there is a minor disalignment between the ribbon representation and the ball & stick representation.
>  
> I remember I have read somewhere by a ribbon related command the Chimera can align the ribbon representation and ball & stick presentation nicely, but I have forgotten where I read the tutorial or introduction.
>  
> Will you please tell me the command to have chimera to get good alignment of the ribbon representation and ball & stick presentation, or tell me the weblink of the corresponding tutorial or reference?
>  
> I am looking forward to getting your reply.
>  
> Smith




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