Rather that using the GUI to read in information, you can use the following command line arguments:
--c cmd to run a command cmd on start up
--script filename to run a script on start up (but see Section Scripting)
--no-state-script don't run the 0-coot.state.scm script on start up.
Don't save a state script on exit either.
--pdb filename for pdb/coordinates file
--coords filename for SHELX .ins/.res and CIF files
--data filename for mtz, phs or mmCIF data file
--auto filename for auto-reading mtz files (mtz file has the default labels FWT, PHWT)
--map filename for a map (currently CCP4-format only)
--dictionary filename read in a cif monomer dictionary
--help print command line options
--stereo start up in hardware stereo mode
--version print the version of coot and exit
--code accession-code on starting Coot, get the pdb file
and mtz file (if it exists) from the EDS
--no-guano don't leave “Coot droppings” i.e. don't write state
and history files on exit
--side-by-side start in side-by-side stereo mode
--update-self command-line mode to update the coot to the latest
pre-release on the server
--python an argument with no parameters - used to tell Coot that
the -c arguments should be process as python (rather than as scheme).
--small-screen start with smaller icons and font to fit on small
screen displays
--zalman-stereo start in Zalman stereo mode
So, for example, one might use:
coot --pdb post-refinement.pdb --auto refmac-2.mtz --dictionary lig.cif