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

Cynthia Lee Page cynthia.page at colorado.edu
Wed Apr 14 14:03:42 PDT 2021

Thanks Elaine!

These files were all mol maps that were made originally using 15 res, so the voxel size was 5. Then resized using a script from Relion, relion_image_handler , with options --rescale_angpix and —new_box.

This suggests my relion script did not work, however as you say the voxel size is what I would have expected if the script did the job. I believe the box outlines are fine, I "turn them on" one at a time with check box (used three different colors, white, yellow, aqua), or with your command line, and in both cases here they are right on top of each other.

Here’s a picture. I will do as you have suggested to report a potential bug, but honestly it is probably me :)



[cid:CFDC301F-1AF7-46CA-BA58-CBC8C8A6946F at colorado.edu]

On Apr 14, 2021, at 2:23 PM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

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<mailto:cynthia.page at colorado.edu>> wrote:

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,

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