[Chimera-users] centroid trace problems

Francesco Pietra chiendarret at gmail.com
Sun Jul 31 09:57:15 PDT 2011

"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?

francesco pietra

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