#===================================>
Comments/Notes
#=================>
IMPORTANT: Z-maps and event maps are constructed in a reference frame and aligned back to the crystallographic "native" frame. 
Therefore, all of the maps are suffixed with ".native.ccp4". However, these maps are aligned globally, rather than locally, 
so there may be visual discrepancies between the ligand model and the density in the event map. This does not mean that the
ligand model is wrong, however, and it is just a methodological artefact. This will be corrected in future versions of panddas.

IMPORTANT: The compounds in the <data> directories may not match the compounds in the models, as ligands could have been 
misassigned to crystals. If a compound mismatch is detected, this is corrected in the <models> directories.

Events can be matched to locations in each dataset using the table in meta/pandda_analyse_events.csv

#===================================>
Folder hierarchy
#=================>
|-- reference                 > Contains information pertaining to the reference structure (contains R-free flags)
|
|-- meta                      > Contains various output files from the pandda analysis
|
|-- data                      > Contains the processed diffraction data for all of the datasets
| |-- <dataset_folders>       > Each dataset is stored in a folder labelled with the dataset name
| | |- <label>.aimless.log    > Log file from aimless
| | |- <label>.data.mtz       > Processed diffraction data
| | |- <label>.free.mtz       > Processed diffraction data with R-Free flags transferred from reference dataset
| | |- <label>.dimple.pdb/mtz > Output files from Dimple (using the reference structure and <label>.free.mtz)
| | |- ligand*.pdb,cif        > Ligand files for the dataset -- THIS IS THE COMPOUND THAT WAS ORIGINALLY ASSIGNED TO THE DATASET
|
|-- models
| |-- <dataset_folders>             > Each dataset is stored in a folder labelled with the dataset name
| | |- <label>.final.pdb/mtz        > Final refined structure of the dataset
| | |- <label>.final.stripped.pdb   > Final refined structure of the dataset, with the ground state removed
| | |- <label>-z_map.native.ccp4    > Z-map from PanDDA 
| | |- <label>-event_*.native.ccp4  > Event maps, labelled by event and the associated BDC
| | |- ligand*.pdb,cif              > Ligand files for the dataset -- THIS IS THE COMPOUND THAT HAS BEEN MODELLED IN THE DATASET

#===================================>
> meta/dataset_ligands.csv
#=================>
This csv file contains the ligands for each dataset. The soaked compound is the compound (that was thought to have been) added to 
the crystal. The modelled compounds are the actual compounds that have been modelled. If these differ from the soaked compound, 
they commonly come from neighbouring datasets (up to two datasets away).

#===================================>
> meta/ligand_scores.csv
#=================>
This csv file contains the validation scores for each of the modelled ligands. 

#===================================>
> meta/pandda.log, meta/pandda.eff
#=================>
log files and parameters from pandda run

#===================================>
> meta/pandda_analyse_events.csv
#=================>
dtag                        : dataset name/label
event_idx                   : index/counter of the identified events for a datasets. Starts from 1.
site_idx                    : index/counter of the identified sites (groups of events) on the protein. Starts from 1.
1-BDC                       : the identified BDC for this event. Recorded as 1-BDC.
z_peak                      : the peak value of the Z-scores in the Z-cluster
z_mean                      : the mean value of the Z-scores in the Z-cluster
cluster_size                : the size of the Z-cluster
x,y,z                       : coordinates of the Z-peak in the native coordinate frame
refx,refy,refz              : coordinates of the Z-peak in the reference coordinate frame
high_resolution             : resolution of highest-resolution reflection
low_resolution              : resolution of lowest-resolution reflection
r_free,r_work               : r-free and r-work of the Dimple output for the dataset
rmsd_to_reference           : rmsd of the dimple solution to the reference structure (c-alphas only)
space_group                 : space group of the dataset
uc_a,uc_b,uc_c              : unit cell lengths
uc_alpha,uc_beta,uc_gamma   : unit cell angles
uc_vol                      : unit cell volume
analysed_resolution         : resolution at which this dataset was analysed
map_uncertainty             : estimated map uncertainty of this dataset, estimated by deviation from the mean map
obs_map_mean,obs_map_rms    : mean and rms of the scaled maps
z_map_kurt                  : kurtosis of the z-map 
z_map_mean                  : mean of the z-map
z_map_skew                  : skew of the z-map
z_map_std                   : std of the z-map