

How to get started with MLFSOM

First, you need some structure factors:

  you can use any *.mtz file containing an "F" and "DANO" you like
  if you want completely "fake" F and DANO, then you can use the
  ano_sfall.com program to generate them from a PDB file.

# generate some fake data from a Gd-soaked lysozyme structure
./ano_sfall.com energy=12660 1H87.pdb

# This will automatically pick bulk solvent parameters, resolution, etc
# you can override most of these.

# generate some fake data from a Gd-soaked lysozyme structure
./ano_sfall.com energy=12660 refined.pdb 1.2A solvent_B=35

# Run ano_sfall.com with no arguments for online help.

# whatever input MTZ file you choose, it should be named "pristine.mtz"
mv ideal_ano.mtz pristine.mtz

# mlfsom also needs a file called "refined.pdb" in the current working
# directory to compute diffuse scattering and Compton scattering
cp 1H87.pdb refine.pdb


# you can optionally simulate specific radiation damage by creating a
# "decayed.mtz" file.  As opposed to the undamaged "pristine.mtz"

grep -v " GD " refined.pdb >! damaged.pdb
./ano_sfall.com energy=12660 damaged.pdb 1.2A solvent_B=35

mv ideal_ano.mtz decayed.mtz


# next, you may want to go over the mlfsom.params most options are
# specified here, and this file is "sourced" by mlfsom.com when it runs
vi mlfsom.params

# now you can run mlfsom.com to generate some fake images.  A mosflm-style
# orientation matrix may be specified on the command line.  You can
# override most defaults on the command line.  
./mlfsom.com frames=100 example.mat

Run mlfsom.com with no arguments to get online help.


