[Chimera-users] display of glycine atoms

Levandoski, Mark LEVANDOS at Grinnell.EDU
Tue Jun 11 14:38:18 PDT 2013

Hi Elaine - 

Excellent, through your suggestions I was able to display what I wanted to do. Thank you very much. In general I probably just need to spend more time with the program, but I really appreciate you getting back to me so quickly.


Mark M. Levandoski
Associate Professor of Chemistry
Grinnell College

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Tuesday, June 11, 2013 4:02 PM
To: Levandoski, Mark
Cc: 'chimera-users at cgl.ucsf.edu'
Subject: Re: [Chimera-users] display of glycine atoms

Hi Mark,
Neither of these issues are specifically related to version, but are general behaviors that have been the same for some time.

(a) ribbons do not have elements; each separately colorable "piece" represents all the backbone atoms of one residue (N,CA,C,O in the case of an amino acid) so coloring by element does not apply.  You can color that piece whatever color you want, just not "by element."

(b) showing ribbon by default suppresses display of the backbone atoms, and glycine is only backbone atoms, i.e. glycine doesn't have a sidechain. 

The "ribbackbone" command enables showing both ribbons and backbone atoms at the same time, which may or may not be what you actually want to do.  More discussion of this issue here:

I hope this clarifies,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Jun 11, 2013, at 1:12 PM, "Levandoski, Mark" <LEVANDOS at Grinnell.EDU> wrote:

> Hello there -
> I recently got a new office machine and had to reload Chimera. Although I do not recall the number of the version I had used in the past, empirically I can tell that this is some updated version. My problem is that I am trying to display various residues of a protein selectively as space-filling ("sphere") on a ribbon frame. One residue of interest is a glycine. This version of Chimera seems incapable (or I am incapable of discovering how!) of displaying the various atoms belonging to this glycine residue. All other residues seem fine. Is this a glitch? Am I doing something wrong? For comparison, I have every confidence that this should work because with my older version of the program I was able to generate just such a view.
> Thank you very much in advance for the help, Mark
> P.S. By selecting the glycine of interest I am able to color the strip of ribbon by preset color, but not by element.

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