[Chimera-users] centroid trace problems

Elaine Meng meng at cgl.ucsf.edu
Sun Jul 31 10:14:19 PDT 2011

Hi Francesco,
I'm glad to hear you like the centroid feature!

If you want only a specific residue, use only the residue number.  If  
you use both the name and the number you will get all of the residues  
with the name, PLUS all of the residues with the number.  For example,  
if there are three histidines HIS 126,152, and 225,


will specify all three histidines.  To specify only HIS 225, use


I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 31, 2011, at 9:57 AM, Francesco Pietra wrote:

> hello:
> "centroid" works fine to me in getting the trace of a moving molecule
> in and out of a protein, using command
> define centroid radius 0.2 color red :residuename
> when the residue is unique. In fact, the method has produced
> extraordinarily illustrative (I am using the words of the referee) in
> a paper that will appear shortly on Chemistry & Biodiversity. Now I
> have three diatomic molecules, only one of which is made moving
> around. In this case
> define centroid radius 0.2 color red :residuename:residuenumber
> for the moving residue does not work. What happens is that "red balls"
> for the specified residue are being accumulated at the place of origin
> of the residue, while the residue is leaving the protein as a short
> bar, not a ball. Could that be fixed in the above command?
> thanks
> francesco pietra

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