The zoom command of course gives the pixels size shown on the screen (what else could it give you). I’m guessing our graphics window on the screen was not 4000 by 4000 pixels, you can find out what it really is (or you can set it) with the windowsize command. So if your graphics window size on screen is 1000 by 1000 and your image is 4000 by 4000 and zoom reports pixel size 0.4 Angstroms then the image will have pixel size 0.1 Angstroms.

Tom

On Jul 31, 2019, at 4:43 PM, Yazan Abbas <yazan.abbas@gmail.com> wrote:

Hi,

I am trying to create a scale bar using the following method:
camera is set to ortho
save image image.png width 4000 height 4000 transparentBackground true
check pixel size in chimeraX using the zoom command (which shows Pixel size at center of rotation is 0.178)
in imageJ, set the scale to be 0.178Å/pixel which turns into 5.618 pixels/Å
Show scale bar of desired in length in ImageJ
However, the resulting scale bar looks unusually small given the dimensions of my particle. Have I misunderstood something about the pixelSize settings? The user guide doesn't say anything about pixelSize when one of or both of width and height are specified in the same image command, so I assumed the pixel size of the saved image would be the same as in the graphics window.

Thanks,

Yazan
_______________________________________________
ChimeraX-users mailing list
ChimeraX-users@cgl.ucsf.edu
Manage subscription:
http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users