[Chimera-users] Pixel size/box size and map display

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 14 13:23:24 PDT 2021

Hi Cynthia,
The question is:  does Chimera know they have different pixel sizes?  

(How do you know that they have different pixel sizes.... is it set or reported in Relion?)

To check or adjust pixel size of maps in Chimera, use Volume Viewer menu "Features... Coordinates" to show map Coordinates settings in the Volume Viewer dialog.  These include Voxel size.  You can see the current values and optionally enter different ones to change them.

Volume Viewer

...and its Coordinates settings:

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 14, 2021, at 1:15 PM, Cynthia Lee Page <cynthia.page at colorado.edu> wrote:
> Hi,
> I have three maps to be used in Relion for reference models. All of these maps are different in pixel size and box size, however they display as the same size in Chimera, with the same size outline box. The voxel size in volume viewer is correct according to the pixel size I designated in Relion_image_handler. I assumed that these maps would be different in size since they have different pixel sizes and box sizes. 
> Can someone set me straight on this?
> Many thanks,
> Cynthia

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