===== How to Run EMReady =====

[[http://huanglab.phys.hust.edu.cn/EMReady/|EMReady - Huang Laboratory]]

=== Load the program : ===
On your GPU node
<code>module load sbgrid/emready</code>

=== Usage: ===
<code>EMReady.sh in_map.mrc out_map.mrc [Options] </code>

=== Required arguments: ===
  * in_map.mrc:   File name of input EM density map in MRC2014 format. (not the sharp map !)
  * out_map.mrc:   File name of the output EMReady-processed density map.

=== Options: ===
  * -g  GPU_ID:    ID(s) of GPU devices to use. e.g. '0' for GPU #0, and '2,3,6' for GPUs #2, #3, and #6. (default: '0')
  * -s STRIDE:    The step of the sliding window for cutting the input map into overlapping boxes. Its value should be an integer within [12,48]. (default: 12)
  * -b BATCH_SIZE:    Number of boxes input into EMReady in one batch. (default: 10)
  * -m MASK_MAP:    Input mask map in MRC2014 format. (default: None)
  * -c MASK_MAP_CONTOUR:    Set the contour level of the mask. (default: 0.0)
  * -p MASK_STRUCTURE:    Input structure mask files in PDB or CIF format (default: None)
  * -r MASK_STRUCTURE_RADIUS:    Zone radius in angstroms (default: 4.0)
  * -mo MASK_OUT_PATH:    File path of the output binary mask map. (default: None)
  * --use_cpu:    Run EMReady on CPU instead of GPU.

=== Notes: ===
  - Users can specify a larger STRIDE of sliding window (default=12) to reduce the number of overlapping boxes to calculate. If users run out of memory, they may set it to a larger value. Howerver, since the size of the overlapping boxes is 48×48×48, the value of STRIDE should not exceed 48.
  - By default, EMReady will run on GPU(s). Users can adjust the BATCH_SIZE according to the VRAM of their GPU. Empirically, an NVIDIA A100 with 40 GB VRAM can afford a BATCH_SIZE of 30. Users can run EMReady on CPUs by setting --use_cpu. But this may take very long time for large density maps.