Hi, Could I check if there is a command line version of the "center" button under Origin Index in the Volume Viewer? Thank you! [cid:image001.png@01D2F697.ECEEC010] Warmest Regards, Yong Zi Tan
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@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
Dear Elaine, Thanks so much, that worked! Warmest Regards, Yong Zi Tan
On 7 Jul 2017, at 11:35 AM, Elaine Meng <meng@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@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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Elaine Meng -
Yong Zi Tan