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

[Tom Goddard]

Hi Cynthia,

  This does not seem like a bug.  I would expect the box size to stay the same when Relion changes the pixel size.  For instance if you change the pixel size from 2 Angstroms to 1 Angstrom it probably doubles the number of grid points so the overall size of the map remains the same.

	Tom


> On Apr 14, 2021, at 2:03 PM, Cynthia Lee Page <cynthia.page at colorado.edu> wrote:
> 
> 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 :)
> 
> Cheers,
> 
> Cynthia
> 
> 
> 
> 
> 
>> 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
>> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html <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 <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 <mailto: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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