Hi Tom,
Thanks for the clarification.
Best,
Yazan
On Wed, Jul 31, 2019 at 8:01 PM Tom Goddard goddard@sonic.net wrote:
One other note — if your graphics window on screen is not square and you save the image as square some padding is going to be done which you probably don’t want. So save the image specifying "width 4000” and don’t specify the height — then the height will be chosen to give the same aspect ratio as on screen. Or you can use the "windowsize 600 600” command to make sure your window is square.
Tom
On Jul 31, 2019, at 4:59 PM, Tom Goddard goddard@sonic.net wrote:
Hi Yazan,
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 3. check pixel size in chimeraX using the zoom command (which shows Pixel size at center of rotation is 0.178) 4. in imageJ, set the scale to be 0.178Å/pixel which turns into 5.618 pixels/Å 5. 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