Influence of pump laser fluence on ultrafast myoglobin structural changes

DESCRIPTION OF TAR ARCHIVE CONTENTS
the folder SCRIPTS contains two subfolders: ANALYZE and REFINE
ANALYZE contains python3 scripts for analysis.There are three files:-analyze_pdb.py which contains functions, and-make_figures.py which calls these functions.
In make_figures.py one needs to change the directories at thebeginning of the script so the script can find the files it needs.Moreover, one needs to have numpy, scipy, and matplotlib installed.
As the functions in analyze_pdb cannot handle altlocs, there is a third file: extract_Bloc.py which takes the B altloc atoms out of a pdb file and makes a new file containing only these. In this way, the photolyzed structures, which are stored als altloc B by the refinement script (see below), can be analyzed.

REFINE contains the files needed for multi-copy refinement.
There are several files:
-multicopy_refine performs the multicopy refinement (duh...); it needs to be edited to conform to your file names/directory structure. Instructions are at the top of the file. The script requires python2.7 and phenix. This version will use the automatically determined occupancy for final refinement. The file needs to be adapted when another, preset occupancy is required.
-refine_par.in contains parameters for phenix.refine that are called by multicopy_refine, and needs to be in the same directory.
-the pdb files are the starting structures for multicopy refinement. The "4 and 18 uJ" starting structures are for the 23- and 101 mJ/cm2 case (and the power titration), for the low-fluence data the other dark structures ("1 uJ") need to be substituted. Details of the multicopy refinement scheme are in the publication.

Back in the top folder, the subfolder GEOMETRY contains the .cif file which describes the heme geometry usedfor all refinements. In it, the prior ESDs for the planarity of the heme have been increasedfrom 0.02 to 0.2
The STREAMS folder contains the CrystFEL stream files used for Monte Carlo integration. There are four subdirectories, one for each time series, and a separate one for the power titration.
DARKS contains the refined dark structures as well as the MTZ files with the dark data. 
POWERTITRATION contains the power titration multicopy refinement results, as well as the MTZ files with the integrated data. 
TIMESERIES contains the time series multicopy refinement results.