(input files for this example are on hermione in /home/dave/cns_examples/MIR_phase_L9)
Things you need:
x-ray data; 2) derivative x-ray data; and
3) you must know the coordinates of your heavy atoms, usually obtained
by solving the Patterson map.
First run merge.inp
to merge the native and derivative data
into one hkl file: cns_solve < merge.inp > merge.log &
Next, run scale.inp
to scale the native and derivative data:
cns_solve < scale.inp > scale.log &
coordinates go into ".sdb" files
(see iod.sdb as an example, containing L9 iodine coordinates).
Next, run "ir_phase.inp"
to calculate the phase for each reflection:
cns_solve < ir_phase.inp > ir_phase.log &
ir_phase is a new file called "ir_phase.hkl" which
contains a phase (described by Henderson-Lattmann coefficients) to go
with each observed reflection.
file serves as input to "fourier_map_mir.inp", which
is used to calculate an electron density map.
density map can be improved by solvent flatteining.
To run the solvent flattening program:
cns_solve < density_modify.inp > density_modify.log &
Output is a
new file with modified phase values called "density_modify.hkl" which
a new phase (described by Henderson-Lattmann values) to go with each observed reflection.
Also, a solvent flattened electron density map is output (called "density_modify.map").
Solvent flattened MIR map for L9, using CNS.
examples of "merge.inp", "scale.inp", "ir_phase.inp" and
"fourier_map.inp" and "density_modify.inp" can be found on hermione in
You can copy the files into your
own directory if you want to run them. The required native
and derivative data sets, and heavy atom positions, are also in this same directory.
Also see the file "dave_notes_mir"
in the same directory on hermione.