[Chimera-users] Color surface along an axis

Elaine Meng meng at cgl.ucsf.edu
Thu May 20 10:51:13 PDT 2021

Hi Yanhe,
When you first open data after starting Chimera (and before you moved it), its X axis is left-right, Y is up-down, Z is near-far from viewer position.  Or you can restore that initial orientation with command: reset

Another way to see the axes even after you moved everything is to open the axis object file "XYZ-axes.bild" linked to this page (download as plain text, keep .bild at the end of filename, open in Chimera) to display them in 3D:

Look at the text of the XYZ-axes.bild file to see which axis is which color.

As for the origin point, either you might already know if you are the person who made the map, or you can use the Volume Viewer tool's menu: Features... Coordinates to show the map origin index (this is NOT the coordinates of the origin but instead, the grid units of the map where the 0,0,0 coordinates are) and voxel size, 
...and use those values to calculate what origin coordinates you want to use in Surface Color.

I hope this helps,

> On May 19, 2021, at 7:50 PM, Yanhe Zhao <yanhezhao1990 at gmail.com> wrote:
> Hi Elaine,
> Thanks for the quick reply, it helps a lot.
> How can I show the coordinate axis and know the xyz of one exact position which maybe used as my origin for coloring gradient.
> Thanks again for your help,
> Yanhe
> On Wed, May 19, 2021, 9:08 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Yanhe,
> In Surface Color you would choose coloring by "height"  which actually means by distance from a plane along its normal; the plane can be in any orientation.  You would just need to enter origin and axis values to define the plane.  The default values of these are set to color along map Z (axis 0 0 1).  To color along X instead, change axis to 1 0 0 .
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On May 19, 2021, at 6:49 PM, Yanhe Zhao <yanhezhao1990 at gmail.com> wrote:
> > 
> > I'm trying Tools...Volume Data...Surface Color, have not figured out the one I wanted.
> > Any suggestions would be appreciated.
> > Thanks and cheers,
> > Yanhe
> > 
> >> On May 19, 2021, at 6:42 PM, Yanhe Zhao <yanhezhao1990 at gmail.com> wrote:
> >> 
> >> Hi Elaine,
> >> 
> >> Sorry for my delay as I was trying the ways you described above. Thanks a lot for that.
> >> I have another question as below:
> >> How can I have color gradient along the map dimensions? For example along X.
> >> 
> >> Thanks and best,
> >> Yanhe

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