[Chimera-users] Centering Origin Index on Command Line

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 7 08:35:07 PDT 2017


Hi Yong Zi Tan,
Sorry, I don’t think there is a command that automatically does the same thing as that center button. However, here is an “originIndex” option of the “volume” command to set the values directly. 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dimensions>

Since the center button just specifies the middle of the grid,
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>
… you only have to know the grid size.  For example, if I have a grid size 45 X 41 X 42, the center button sets the origin index to 22 20 20.5   … so I guess you would subtract 1 from each number and then divide by two to get the values to use with the “originIndex” option of the “volume” command.  

Just make sure to test this in a few cases, to confirm that the center button does give you the same values you calculated from the grid size.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jul 6, 2017, at 5:39 PM, Yong Zi Tan <ytan at nysbc.org> wrote:
> 
> Hi, 
> Could I check if there is a command line version of the “center” button under Origin Index in the Volume Viewer? Thank you!
>  
> <image001.png>
>  
> Warmest Regards,
> Yong Zi Tan




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