[Chimera-users] centroid trace problems

Francesco Pietra chiendarret at gmail.com
Sun Jul 31 22:38:56 PDT 2011

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..


On Sun, Jul 31, 2011 at 7:14 PM, Elaine Meng <meng at cgl.ucsf.edu> 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 at 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

More information about the Chimera-users mailing list