update readmes and paths

README.md

@@ -1,34 +1,35 @@
 # dw-examples
 
-Examples of merging crystallographic intensities with a bivariate prior
+This folder contains four examples of merging crystallographic intensities with a bivariate prior:
 
-## Setup 
+- [time-resolved Laue crystallography of the photoactive yellow protein](pyp/README.md)
+- [anomalous diffraction from serial XFEL crystallography of thermolysin](thermolysin_xfel/README.md)
+- [anomalous diffraction from Laue crystallography of NaI-soaked lysozyme](lysozyme/README.md)
+- [fragment screening monochromatic data of Nsp3 Mac1](dfs/README.md)  
+
+Every example includes scripts to run `careless` as well as to analyze the outputs in order to reproduce the figures in the double-Wilson manuscript. For every example, there is a `README.md` that describes the contents of each example folder.  
+
+## requirements 
 
-To run much of the scripts and notebooks in this repository, [Careless](https://github.com/rs-station/careless) and [rs-booster](https://github.com/rs-station/rs-booster) must be installed. Many scripts activate a conda environment with Careless installed, e.g.:
+To run much of the scripts and notebooks in this repository, [Careless](https://github.com/rs-station/careless) and [rs-booster](https://github.com/rs-station/rs-booster) must be installed. See both repositories for installation instructions. Many scripts activate a conda environment with Careless installed, e.g. [run_ccs.sh](pyp/run_ccs.sh) in the `pyp` folder:
 
-[run_ccs.sh](pyp/run_ccs.sh)
 ```
 #please indicate your desired careless environment here!
 eval "$(conda shell.bash hook)"
 conda activate careless
 ```
 Please change the name of the conda environment as needed. 
 
-Additionally, some scripts require sourcing Phenix, e.g.: 
-[run_ccs.sh](thermolysin_xfel/scripts/run_ccs.sh)
+Additionally, some scripts require sourcing Phenix, e.g. [launch_refinement.sh](thermolysin_xfel/scripts/launch_refinement.sh) in the `thermolysin_xfel` folder: 
+
 
 ```
 # source your copy of phenix here!
-source /n/holylfs05/LABS/hekstra_lab/Lab/garden/phenix/phenix-1.20.1-4487/phenix_env.sh
+source ../../../../../../phenix-1.20.1-4487/phenix_env.sh
 ```
 Please change the path of the phenix environment file as needed. 
 
 Finally, all jobs were run on a computing cluster, so certain Careless scripts require `slurm` to run. 
 
-## Examples
-For every example, there is a `README.md` that describes the contents of each example folder. Additionally, every example includes scripts to run `careless` as well as to analyze the outputs in order to reproduce the figures in the double-Wilson manuscript. The examples are: 
 
-- [time-resolved Laue crystallography of the photoactive yellow protein](pyp/README.md)
-- [anomalous diffraction from serial XFEL crystallography of thermolysin](thermolysin_xfel/README.md)
-- [anomalous diffraction from Laue crystallography of NaI-soaked lysozyme](lysozyme/README.md)
-- [fragment screening monochromatic data of Nsp3 Mac1](dfs/README.md)  
+

dfs/README.md

@@ -5,7 +5,7 @@ This folder contains instructions and scripts for processing an Nsp3 Mac1 fragme
 2. inspect CCpred and difference map peak heights.
 
 
-We start with MTZ files found in `./20221007_unscaled_unmerged`. These were converted from unmerged `.hkl` files generously gifted by Galen Correy, for (Schuller et al. 2021). 
+We start with MTZ files found in `./20221007_unscaled_unmerged`. These were converted from unmerged `.hkl` files provided by Galen Correy, for (Schuller et al. *Sci. Adv.* 2021, DOI: 10.1126/sciadv.abf8711). 
 
 To run `careless`, we use the script `careless_runs/slurm-dw-array-grid.sh`, which starts a `slurm` batch array job. This job requires `careless_runs/slurm_params.txt`, in which we vary the double-Wilson `r` value across the individual `careless` runs.  To call using slurm: 
 
@@ -31,4 +31,6 @@ Then, we evaluate the quality of the `careless` results in the jupyter notebook
     - `hkl2mtz.sh`: a script that uses careless to convert `.hkl` files to `.mtz` files. 
     - `make_diffmap_all.sh`: A script that uses `rs-booster` to compute difference maps given a folder with `careless` runs in it. 
     - `make_diffmap_indiv.sh`: A script that uses `rs-booster` to computes difference maps of a single `careless` run. 
-    - `run_ccs_all.sh`: A script that computes CCpred given a folder with `careless` runs in it. 
+    - `run_ccs_all.sh`: A script that computes CCpred given a folder with `careless` runs in it. 
+- `Inspect_Careless_param_grid-DFS.ipynb`: a notebook for evaluating the quality of the `careless` results.
+- `compute_pandda_peak_height.ipynb`: a notebook for peak height calculation of the Z-maps.