[Chimera-users] Centering Origin Index on Command Line

Yong Zi Tan ytan at nysbc.org
Mon Jul 10 07:38:12 PDT 2017


Dear Elaine,

Thanks so much, that worked!

Warmest Regards,
Yong Zi Tan

> On 7 Jul 2017, at 11:35 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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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