This feature has been merged into the official DIALS distribution; this repository will no longer be updated.

This program reconstructs reciprocal space from diffraction images. The orientation matrix is not necessary; only diffraction geometry is required.

This program is inteded to help detection and visualization of pathologies such as multiple-lattice, twinning, modulation, diffuse scattering and high background. It is also useful for education.

1. Build cctbx and DIALS.

   1. get latest cctbx as described in http://cctbx.sourceforge.net/current/installation.html#using-the-cctbx-svn-repository but do NOT configure yet.

   2. fetch latest DIALS from http://sourceforge.net/p/dials/code/HEAD/tree/ into cctbx_project directory

   3. configure as described in the page above but with 'dials' instead of 'mmtbx'

       mkdir build 
       cd build 
       /your/choice/bin/python ../sources/cctbx_project/libtbx/configure.py dials 
       source setpaths.csh 
       make 
      

2. Clone this repository to cctbx_project directory, where you have cctbx, dstbx, dials folders among others.

3. Go to your cctbx build directory in step 1.3

4. Run

       libtbx.configure recviewer
       make
   

First, you have to setup environmental variables.

source /path/to/build/directory/setpaths.sh

Then,

recviewer.run --map_file output.ccp4 [--max_resolution 6] [--grid_size 192] [--reverse_phi] image_???.cbf

(Options in blankets can be omitted.)

The output is in CCP4 map format (also known as MRC format). Thus, you can use PyMOL, Chimera, Coot for visuallization. I suggest PyMOL's volume rendering, provided that you have a decent video card.

1. Start PyMOL

2. load output.ccp4 (if the file extension is .map, you have to add ', format=ccp4')

3. Click [A] button and select [Volume]-[default].

4. Click [Volume] button in the menu window. Adjust transfer function.

5. For better quality of rendering, try

       set volume_layers, 512 
   

   (or even more, but it makes rendering slower)

Depending on the dataset, you might need

set volume_data_range, 10

The default is 5.

Same as cctbx and DIALS. That is, BSD license.