Input Data issues
Q. MAINMAST terminated with the error.
"Fortran runtime error: Index '301' of dimension 2 of array 'dmap' above upper bound of 300".
A. This error was caused by the limitation of memory space in MAINMAST program. In order to reduce the size of map file, we can use "relion_image_handler" command. The size of map should be smaller than 15-*150*150.
Sample command: Shift map to their center-of-mass and change voxel size to 100*100*100.
relion_image_handler --i INPUT.mrc --new_box 100 --o OUTPUT.mrc --shift_com true
Q. I do not have the relion program in my PC. How can I reduce the size of EM map?
A. If you have a reference pdb file. You can extract the regions within a specific distance of the currently selected atoms (or chains/molecules) by "zone tool" in UCFS Chimera.
Example (extract density data around chain A in PDB file)
- Select chain A:
[Chimera menu] select > Chain > A
- Segment out around chain A:
[Volume Viewer Menu] Features>Zone
Click [Zone] botton.
- Save the segmented map:
[Volume Viewer Menu] File>Save Map as...