#!/bin/sh

# FOR UNIX USERS

# Create the directory structure for a SPIDER reconstruction project,
# based on batch files from "Three Dimensional Reconstruction of 
# Single Particle Specimens using Reference Projections"
#
# Copy this file to the top level directory of your project, with a
# name such as "makedirs".
#
# Make it executable with:
#   % chmod 755 makedirs
#
# Then execute the script by typing its name at the Unix prompt:
#   % makedirs
#
# NOTE: this script makes directories for only 6 defocus groups. If 
# additional defocus groups are used, their directories must be added. 


mkdir Micrographs

mkdir Power_Spectra
  mkdir Power_Spectra/power

mkdir Particles
  mkdir Particles/coords
  mkdir Particles/good
  mkdir Particles/win

mkdir Alignment
  mkdir Alignment/ali
  mkdir Alignment/apmq
  mkdir Alignment/avg
  mkdir Alignment/groups
  mkdir Alignment/prj
  mkdir Alignment/selectotal
  mkdir Alignment/df001
    mkdir Alignment/df001/select
  mkdir Alignment/df002
    mkdir Alignment/df002/select
  mkdir Alignment/df003
    mkdir Alignment/df003/select
  mkdir Alignment/df004
    mkdir Alignment/df004/select
  mkdir Alignment/df005
    mkdir Alignment/df005/select
  mkdir Alignment/df006
    mkdir Alignment/df006/select


mkdir Refinement
  mkdir Refinement/ctf
  mkdir Refinement/final