DireX  v0.7.1  - Real-space Structure Refinement

(c) Copyright 2006-2019 Gunnar F. Schroeder 
    with contributions from Benjamin Falkner
    and Zhe Wang


INTRODUCTION
--------------------------------------------

DireX is a low resolution structure refinement program. 
The programs implements the Deformable Elastic Network (DEN) 
approach to reduce over-fitting and a very efficient 
geometry-based conformational sampling algorithm (based on 
CONCOORD; de Groot, et al., Proteins 29: 240-251 (1997)).
It should be noted that DEN has NOTHING to do with normal
modes.  


Experimental data that can be used for refinement are:

 * Density maps 
         obtained from X-ray Crystallography, 
         Electron Microscopy (cryoEM), or 
         Small-angle X-ray Scattering (SAXS)

 * General distance restraints
         obtained from NMR, or FRET experiments. 


If you publish or present work based on DireX, please
cite our publication:

  G.F.Schroder, A.T.Brunger, and M.Levitt
  'Combining Efficient Conformational Sampling with a 
  Deformable Elastic Network Model Facilitates Structure 
  Refinement at Low Resolution'
  Structure, Vol 15, 1630-1641, 13 December 2007

DireX uses a cross-validation approach which is published here:

  Benjamin Falkner and Gunnar F. Schroder
  Cross-validation in cryo-electron microscopy based structural modeling 
  PNAS (2013) 110(22):8930-8935.



INSTALLATION
--------------------------------------------

1. Unpack direx-0.7.1.tgz by:
   $> tar -xvzf direx-0.7.tgz

2. Go to the src directory 
   $> cd src

3. And run make to compile DireX
   $> make

   The executables will be copied to  direx-0.7.1/bin

   You can either just copy the executables 'direx' to your 
   favorite directory or add the direx-0.7.1/bin directory to your 
   PATH environment variable.

   If you use Bash, add a similar line your .bashrc :
   export PATH=$PATH:/home/gunnar/programs/direx-0.7.1/bin/

   or if you use csh, add a similar line to your .cshrc :
   setenv PATH $PATH:/home/gunnar/programs/direx-0.7.1/bin/


Install Chimera Plug-in

   1. Open Chimera
   2. Go to Favorites->Preferences
   3. Select "Tools" as the Category
   4. Click on "Add..." and select the direx-0.7.1 folder
   5. Restart Chimera.  
   6. The DireX GUI should now be under Tools->Volume Data


LICENSE
--------------------------------------------
The code is published under GPLv3. 


BUG REPORTS AND MORE INFORMATION
--------------------------------------------

For questions, suggestions, bug reports, etc. 
please post at
     https://simtk.org/forum/?group_id=186
        
  or send an email to 
     gu.schroeder@fz-juelich.de

More information can be found here:
     http://www.schroderlab.org/software/direx/index.html