[Chimera-users] showing backbone for some residues and not others

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 6 09:36:20 PST 2016


Hi Arthur, 
I remembered one more “trick” — instead of using ribbackbone on a single structure, you could open the same structure twice:

In one copy of the structure, show ribbons, and show the residues for which you want to see only the sidechains attached to the ribbon (no ribbackbone).

In the other copy of the structure, do not show any ribbons.  Show only the atoms of residues for which you want to show backbone atoms.

The atoms from the second copy could still be floating away from the ribbon of the first copy, but at least the sidechain-only residues (also from the first copy) would be attached to the ribbon.
Best,
Elaine

> On Dec 5, 2016, at 3:12 PM, A G Szabo <agszabo at bell.net> wrote:
> 
> Elaine
> 
> Thank  you for your assistance once again. If  you ever have need of some supportive comments in order to ensure grant support I would be very willing to provide it.
> 
> arthur
> 
> -----Original Message-----
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
> Sent: December-05-16 5:26 PM
> To: A G Szabo
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] showing backbone for some residues and not others
> 
> Hi Arthur,
> You are right, you have hit one of the limitations of  Chimera:  it is not possible to have ribbackbone on only part of a model, and when it is turned on you can only show the “real” positions of the backbone atoms which may appear as detached from the ribbon.
> 
> Two possibilities are to show the CA as a bigger ball so that the detachment is not so obvious, or to use the cardinal spline for the ribbon which goes through the real CA atom positions, as mentioned earlier.
> 
> This issue of CA floating away from the ribbon and the ways to (try to) solve it are discussed in the manual here:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset>
> 
> Selection Inspector is simply a dialog that shows the settings of the things you have selected currently, and allows you to change their settings by choosing or entering different values.  If using this dialog, you don’t have to remember the commands.  For example,  instead of using “ribbackbone” command you can just select any atom in the model and use the Selection Inspector: in that dialog “Inspect: Molecule model” and then change its setting “ribbon hides backbone atoms” between true and false.
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>
> 
> Similarly, then I don’t have to explain the commands to change the ribbon from B-spline to cardinal spline… Instead, using the Selection Inspector  and inspecting “Molecule model” you can change the settings for “ribbon spline” and “ribbon (cardinal) smoothing”.
> 
> Best,
> Elaine




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