To allow the user to then use IMOD for the extractions instead of PyCresta, please also store .coords files (i.e., IMOD model text file with x,y,z coordinates in pixel units (!) ) in respective subcoord_files/ directories.
In the Information box in the Re-extraction menu, please add:
After completion of the picking of coordinates, the coordinates are stored in subcoord_files/ directories as both .cmm (ChimeraX x,y,z coordinates in Angstroms) and as .coord (IMOD model x,y,z text files in pixel units).
To perform the extraction with PyCresta using the full tomograms, push the Re-extraction button.
axelbrunger
commented
9 months ago
To allow the user to then use IMOD for the extractions instead of PyCresta, please also store .coords files (i.e., IMOD model text file with x,y,z coordinates in pixel units (!) ) in respective subcoord_files/ directories.
In the Information box in the Re-extraction menu, please add:
After completion of the picking of coordinates, the coordinates are stored in subcoord_files/ directories as both .cmm (ChimeraX x,y,z coordinates in Angstroms) and as .coord (IMOD model x,y,z text files in pixel units).
To perform the extraction with PyCresta using the full tomograms, push the Re-extraction button.
You may also perform the extraction with IMD using the direct reconstruction method "subtomosetup"( https://bio3d.colorado.edu/imod/doc/man/subtomosetup.html).