[Chimera-users] center of molecule

[Elaine Meng]

Hi Bala,
Ah, yes -- focus ignores parts that are not displayed.  The previous  
explanations presumed that all the atoms you want to use in the  
calculation are also displayed.  You could just use the "all atoms"  
preset or command "display" to show all atoms, or you could just  
include the command "display sel" after selecting.

Closing and restarting the session wouldn't affect this issue.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



On Dec 18, 2009, at 2:36 PM, Bala subramanian wrote:

> Elaine,
>
> Sorry for repeating the post. The previous post says that i can get  
> the centroid by typing the following commands.
> I opened a pdb file (attached) in Chimera. I typed sel, reset,  
> focus sel. Then i got the centroid as 28,31,31. I closed the  
> session and opened the molecule again and gave Actions --> Atombs/ 
> Bonds --> show to display all the atoms. Then i typed the same  
> commands sel --> reset ---> focus sel. the calculated centroid was  
> 31.3,30.9,30.8. Why am i getting a slightly different centroid in  
> this case ?
> Bala
> On Fri, Dec 18, 2009 at 6:38 PM, Elaine Meng <meng at cgl.ucsf.edu>  
> wrote:
> Hi Bala,
> You asked the same question earlier this year!  Here is the answer:
>
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/ 
> 003648.html>
>
> 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 Dec 18, 2009, at 8:40 AM, Bala subramanian wrote:
>
> Friends,
> Is is possible to find the central x,y,z coordinates of a pdb file  
> in chimera.
> Bala
>
>
> <test.pdb>
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