This directory contains codes that one can used to run structure 
refinement using 
1) projection matching  (runali3d_d)
2) unified approach     (rununified)
3) hybrid of projection matching and unified approach (runhybrid)
====================================================================

COMPILING THE CODES
-------------------

Before using these codes, you must install sparx (which contains
this directory) correctly. Also make sure MPI is properly installed
on your system.

To generate all three executables, type 

make 

at the command line.  You can generate each individual executable
by typing, for example,

make rununified


RUNNING THE CODES
-----------------

1. To run the projection matching refinement, simply type 

   mpirun -np <np> runali3d_d -data=<stack of image> -model=<initial model> 

   on the command line, where 

      <np>               is the number of processors you want to use.
      <stack of images>  is the name of the hdf file that contains
                         experimental images.
      <initial model>    is the name of the volume file that contains
                         the intial 3-D model. 

   More options will be allowed in future versions.

2. To run the unified refinement, type

   mpirun -np <np> rununified -data=<stack of image> -model=<initial model> \
   -param=<initial angles and shifts>

   on the command line, where

      <initial angles and shifts> refers to an ASCII file that looks like

       -31.6500   26.9880  151.5600         0         0
        14.5040   76.8650   40.3510         0         0
       -43.7830   11.4940  209.0100         0         0
        35.3790   64.2090  307.6300         0         0
        18.5550   27.7880  318.7800         0         0
        18.8660   91.5450  136.1000         0         0
      ....

   The first three columns of the file contain intial guesses to 
   Euler angles in SPIDER format.  The last two columns contain 
   initial guesses to the horizontal and vertical shifts.
    
   More options will be allowed in future version.

3. The syntax for running the hybrid refinement is the same as that
   of the projection matching refinement.

   mpirun -np <np> runhybrid -data=<stack of image> -model=<initial model> 
