[Chimera-users] Fwd: centroid trace problems

Elaine: the sole chance would be to use the ID number, which, of course, is unique even in my case. I had looked around if it were possible. Not found. The residue consists of two ID numbers. francesco ---------- Forwarded message ---------- From: Francesco Pietra Date: Mon, Aug 1, 2011 at 7:38 AM Subject: Re: [Chimera-users] centroid trace problems To: "chimera-users@cgl.ucsf.edu BB" Hi Elaine: I could not use the residue number. This is a patched couple psf/pdb, where the various parts are bound together to establish chemical bonds within the enzyme active center. The various groups maintain the original residue number, which means that there are various different residue with the same number, and this applies in particular to the residue of my interest.. francesco On Sun, Jul 31, 2011 at 7:14 PM, Elaine Meng wrote:

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,

:his:225

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

:225

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D.                          meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco                     http://www.cgl.ucsf.edu/home/meng/index.html

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