Documentation for shelx2map


shelx2map reads a .phs- or .fcf-file ( LIST 6 only!) and converts them to ccp4 map format. This map can then be read into pymol for image rendering.


Please note that from its next release, shelx2map will be available with CCP4.

shelx2map is distributed under the GNU General Public License. Please contact me if this license is not suitable for your purposes.

Shelx2map requires Kevin Cowtan'sClipper library and either CCP4 or Morten Kjeldgaard's gpp4 libraries to be installed.

If you compile shelx2map for other platforms or operating systems I would appreciate a copy for redistribution.



without command line options show a short usage summary:
* shelx2map - convert shelx .fcf and .phs files to                            *
*             to ccp4-format for use in e.g. pymol.                           *
* (c) Tim Gruene, 7/2012                                                      *
Usage: shelx2map [OPTIONS] inputfile[.fcf] [fa_file]
       inputfile:   fcf-file (LIST 6 only) with or without suffix
       fa_file:     use Fa and phi = phicalc - alpha for 
                    creating an anomalous map
       -o filename: explicitly sets output filename
                    unset: derived from input filename + '.map'
       -m N:        integer weight for fcf-files:
                    m=0: |Fo|-|Fc| map
                    m>0: m|Fo| - (m-1)|Fc| map
                    unset: create both difference map and 3|Fo| - 2|Fc| map
       -w w      :  downweight weak data with Fc^4/(Fc^4+w*sig(Fo)**4)
                    without '-w', weighting with w=1.0 is applied.
       -r r      :  set rate for map sampling (default: 1.5)

   or: shelx2map [OPTIONS] inputfile[.phs]
       inputfile  : phs-file with or without suffix
       -o mapname : explicitly sets output filename
                    unset: derived from input filename + '.map'
       -s pdbfile : MANDATORY: source of spacegroup and cell from CRYST1
       -f         : Do NOT weight F with FOM
       -w w       : downweight weak data with 1/(1+w*(sig(Fo)/F)**4)
                    implies '-f', i.e. FOM is not applied
       -r r      :  set rate for map sampling (default: 1.5)
       -h /-?:      print this help message

Tim Gruene

Last modified: Mar 25, 2020 22:42