[Chimera-users] Color surface along an axis

[Yanhe Zhao]

Hi  Elaine,
Thank you so much, that help me a lot and I made it.
Have great weekend.
Best,
Yanhe

Elaine Meng <meng at cgl.ucsf.edu> 于2021年5月20日周四 下午12:51写道：

> 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
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html>
>
> 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:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html>
>
> 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,
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates
> >
> ...and use those values to calculate what origin coordinates you want to
> use in Surface Color.
>
> I hope this helps,
> Elaine
>
> > 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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