[Chimera-users] How to

[Elaine Meng]

The command "ribbackbone" is the only method I know to show both the backbone atoms and the ribbon, and it gives the same result as opening the same structure twice and showing one as ribbon, the other as backbone atoms.

With this method, the atoms are not necessarily floating away from the ribbon, it is only possible that some of them will be off the ribbon, while many of them may match the ribbon pretty well.  Showing them as balls or spheres makes them bigger and more likely to touch the ribbon.  So from your picture, it still seems to me that "ribbackbone" is what you used -- especially since I can't think of any other way to display backbone atoms and ribbon together!
Best,
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 Feb 28, 2011, at 12:37 PM, M. Amin Arnaout wrote:

> Thanks, But I was able to show Calpah and ribbon WITHOUT  position shift of
> the latter using Chimera. I do not remember how I did it (see attached).
> Hope you can help.
> 
> 
> On 2/8/11 12:50 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
> 
>> Hello,
>> I believe this has been the same for many versions -- the default is to hide
>> backbone atoms where ribbon is shown.
>> 
>> However, you can show backbone atoms and ribbon at the same time after you use
>> the command "ribbackbone."  Show the command line (under Favorites menu), then
>> enter the command ribbackbone, then display whichever atoms you wish.
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html>
>> 
>> It may not look very good when you are showing the backbone atoms and the
>> ribbon for the same residue, because the atoms may be "floating" away from the
>> ribbon.  The ribbon is a smoothed path and in some places it does not follow
>> the atoms closely.  More discussion of this issue, in case you are interested:
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonst
>> yle.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 Feb 7, 2011, at 12:26 PM, M. Amin Arnaout wrote:
>> 
>>> I am running Cimera 1.5.2 on Mac. I am now unable to show a cabonyl O, N or
>>> CA  of a residue while ribbon is also displayed. Could do that in the earlier
>>> version.
>>> 
>> 
> 
> 
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