[chimerax-users] pixel size

[Yazan Abbas]

Hi Tom,

Thanks for the clarification.

Best,

Yazan

On Wed, Jul 31, 2019 at 8:01 PM Tom Goddard <goddard at 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 at 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 at gmail.com> wrote:
>
> Hi,
>
> I am trying to create a scale bar using the following method:
>
>    1. camera is set to ortho
>    2. 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
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