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

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 14 13:34:10 PDT 2021

Sorry. I failed to read everything you wrote...  including that you already checked the voxel size in Chimera.  The outline box for a map should reflect grid size (number of points in each dimension) multiplied by the voxel size (physical distance per grid point in each dimension).  If it does not, you could try using Help... Report a Bug and attaching your session with an explanation of what is not matching up.  Include your email address if you would like a response.

My only other ideas:  (1) Make sure you are really showing the outline boxes of all the different maps, not just that for a single map.  E.g. commands

volume all show
volume all showOutlineBox true

 (2) Make sure you are showing the full data, not after cropping.  E.g.

volume all region all


> On Apr 14, 2021, at 1:23 PM, Elaine Meng <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
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
> ...and its Coordinates settings:
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>
> I hope this helps,
> Elaine
> -----
> 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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