[Chimera-users] commands to add red spheres to the ribbon structure

[Elaine Meng]

Hi Bin,
I assumed you were using Chimera.  If you are using ChimeraX, that’s a different story.  Then after opening the structure it would be something like

cartoon suppress false
hide
show :57 at ca
style :57 at ca sphere
color :57 at ca red target a

If you’re using ChimeraX, make sure to say so if you e-mail questions to this list in the future.  Also, there is a separate list you could use instead: chimerax-users at cgl.ucsf.edu

“cartoon suppress false” in ChimeraX is similar to Chimera’s “ribbackbone"

Best,
Elaine

> On Jul 17, 2017, at 12:52 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Bin,
> As far as I know, the same commands as in earlier versions should work.  However, the trick (same as before) is to use the “ribbackbone” command to allow showing backbone atoms at the same time as ribbon.  Then you can show the alpha-carbon as a red ball.  For example, commands:
> 
> open 1hd2
> ribbackbone
> # hide atoms
> ~disp
> disp :57 at ca
> repr sphere :57 at ca
> color red,a :57 at ca
> 
> In the last command, “,a” means atoms-only (not ribbon etc.).  I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> 
>> On Jul 17, 2017, at 10:00 AM, zhangbin <mumu730 at gmail.com> wrote:
>> 
>> Hi Chimera,
>> I would like to know the commands for adding a red sphere to a certain spot in a ribbon structure of a protein (please see the attachment). The command I know worked for older version of the chimera but not this new version 0.1.
>> 
>> Thanks,
>> Bin