Hello,
I have two maps. One from cryosparc @ 1.06 A/pix and another EM-gan sharpened map @ 1.0 A/pix. They are different in size upon visual inspection in chimeraX so I tried relion_image_handler --i cryosparc.mrc --angpix 1.0 --rescale_angpix 1.06 --o cryosparc-rescaled.mrc however, the resulting map is still smaller than the original input. I also tried to rescale in this way to several different angpix values but maps are still not the same.
Is there any command in chimeraX or chimera to play with pix sizes to find the right one?
Thank You and regards,
Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University
Hi Nebojša, See the ChimeraX "volume" command "voxelSize" option: https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions
The Chimera "volume" command has the same option: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dimensions
... and the Chimera Volume Viewer tool (GUI) has the voxel size setting in the Coordinates section (which you would show in the GUI using the Features menu): https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#features
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 28, 2022, at 6:38 AM, Nebojsa Bogdanovic via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
I have two maps. One from cryosparc @ 1.06 A/pix and another EM-gan sharpened map @ 1.0 A/pix. They are different in size upon visual inspection in chimeraX so I tried relion_image_handler --i cryosparc.mrc --angpix 1.0 --rescale_angpix 1.06 --o cryosparc-rescaled.mrc however, the resulting map is still smaller than the original input. I also tried to rescale in this way to several different angpix values but maps are still not the same.
Is there any command in chimeraX or chimera to play with pix sizes to find the right one?
Thank You and regards,
Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University
Hi Nebojša,
When you open a volume file ChimeraX reports the voxel size, for example 2.7 Angstroms in the following example
> open 1080 from emdb Opened emdb 1080 as #1, grid size 100,100,100, pixel 2.7, shown at level 1.68, step 1, values float32
Then if you wanted to change it use
volume #1 voxelSize 2.5
or you can use menu Tools / Volume Data / Map Coordinates and change the voxel size entry in the panel that appears.
Tom
On Jul 28, 2022, at 6:38 AM, Nebojsa Bogdanovic via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
I have two maps. One from cryosparc @ 1.06 A/pix and another EM-gan sharpened map @ 1.0 A/pix. They are different in size upon visual inspection in chimeraX so I tried relion_image_handler --i cryosparc.mrc --angpix 1.0 --rescale_angpix 1.06 --o cryosparc-rescaled.mrc however, the resulting map is still smaller than the original input. I also tried to rescale in this way to several different angpix values but maps are still not the same.
Is there any command in chimeraX or chimera to play with pix sizes to find the right one?
Thank You and regards,
Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
It probably depends what options you use for resizing. You can interpolate the same size grid with more smaller voxels (or fewer larger pixels) or just rescale the sizes of the voxel that are there such that the whole grid changes.
I'm not sure what relon_image_handler does but ChimeraX voxelSize seems to do the second one, which sounds like the one you probably want.
There are also ways to do various resizing operations in Scipion too in case you want to try that.
Best wishes James
Tom Goddard via ChimeraX-users chimerax-users@cgl.ucsf.edu escribió:
Hi Nebojša,
When you open a volume file ChimeraX reports the voxel size, for example 2.7 Angstroms in the following example
open 1080 from emdb
Opened emdb 1080 as #1, grid size 100,100,100, pixel 2.7, shown at level 1.68, step 1, values float32
Then if you wanted to change it use
volume #1 voxelSize 2.5
or you can use menu Tools / Volume Data / Map Coordinates and change the voxel size entry in the panel that appears.
Tom
On Jul 28, 2022, at 6:38 AM, Nebojsa Bogdanovic via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
I have two maps. One from cryosparc @ 1.06 A/pix and another EM-gan sharpened map @ 1.0 A/pix. They are different in size upon visual inspection in chimeraX so I tried relion_image_handler --i cryosparc.mrc --angpix 1.0 --rescale_angpix 1.06 --o cryosparc-rescaled.mrc however, the resulting map is still smaller than the original input. I also tried to rescale in this way to several different angpix values but maps are still not the same.
Is there any command in chimeraX or chimera to play with pix sizes to find the right one?
Thank You and regards,
Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (4)
-
Elaine Meng -
JAMES MICHAEL S1JJRUdFUiA= -
Nebojsa Bogdanovic -
Tom Goddard