PyMOl uses the PrimeX driver to perform map loading and map calculations. PyMOL ships with the optimized Intel MKL libraries for high-speed FFTs.
PyMOL reads the MTZ files. It then parses the header and reads the information. PyMOL will then populate the selection boxes for Amplitudes, Phases, and Weights. Only those columns appropriately typed will be shown in each box. Default column names are preferred and auto-selected. Min and max resolution are read from file.
You can set the default names with the following settings:
default_refmac_names default_phenix_names default_phenix_no_fill_names default_buster_names
The format of each setting is a space-separated string with four values, eg.
"A B C D"
where, A is the default column name of the 2FoFc amplitude; B is the default column name of the 2FoFc phase; C is the default column name of the FoFc amplitude; D is the default column name of the FoFc phase.
default_phenix_no_fill_names does not have FoFc names as it’s not appropriate.
Both 2FoFc maps and FoFc maps have their own default representation when loaded from disk. The default is our new volume representation, but can be set to mesh or surface:
set default_fofc_map_rep, REP set default_2fofc_map_rep, REP
REP can be ‘volume’, ‘isomesh’, or ‘isosurface’.