Macromolecular GUIs for use with SHELX

hkl2map guides experimental phasing with SHELXC/D/E. The graphical diagnostics are particularly useful.

Coot is the program of choice for graphical analysis of the results of experimental phasing and structure refinement.

ARCIMBOLDO locates many possible positions for small fragments using the molecular replacement program PHASER and expands them to the full structure using SHELXE. If one run produces a CC value against the native data that is greater than 25% given data to 2.5Å or better, the structure is almost certainly solved!

Tim Grüne's programs mtz2hkl and mtz2sca read CCP4 .mtz files and write .hkl (for refinement) and .sca (for experimental phasing) using SHELX. His shelx2map converts the .fcf file from SHELXL or the .phs or .pha files from SHELXE into CCP4 format map files that can be used to make publication quality pictures with PYMOL or CCP4mg.

Anna Lübben's program pdb2ins may be used to create a SHELXL format .ins file:
pdb2ins junk.pdb reads junk.pdb and writes junk.ins
pdb2ins @1xyz extracts PDB entry 1xyz from the RCSB and writes 1xyz.ins
pdb2ins @1xyz -b also writes 1xyz.hkl (if the reflections were deposited!)
pdb2ins --help describes further options.
The resulting .ins file uses the new SHELXL facility to handle chain-IDs. It includes restraints for residues and ligands often encountered in macromolecular structures as well as suitable DISP instructions for synchrotron data. In most cases the structure can be refined immediately with SHELXL without the need to change the .ins file written by pdb2ins. pdb2ins is currently only available for 64bit operating systems. Because the file is rather large, it is not included in the Windows file for installing all the programs at once and has to be downloaded sepately from the shelx download site.