Pixel size/box size and map display
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
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@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
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 Thanks, Elaine
On Apr 14, 2021, at 1:23 PM, Elaine Meng <meng@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@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
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 [cid:CFDC301F-1AF7-46CA-BA58-CBC8C8A6946F@colorado.edu] On Apr 14, 2021, at 2:23 PM, Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@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@colorado.edu<mailto:cynthia.page@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
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@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@cgl.ucsf.edu <mailto:meng@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/fram... <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>>
...and its Coordinates settings: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volu... <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@colorado.edu <mailto:cynthia.page@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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participants (3)
-
Cynthia Lee Page -
Elaine Meng -
Tom Goddard