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README.md

 # WatAA
 
-WatAA website code
+Online Atlas of Protein Hydration
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+
+### Usage
+
+WatAA is a dependent project of [Watlas-index](https://gitlab.cesnet.cz/madcatxster/watlas-index). It shall be deployed accordingly to the instructions provided by Watlas-index documentation.
+
+### Configuration
+
+In order to ensure proper functionality of WatAA, a `config.js` file must be present in WatAA's root directory. Content of the file depends on the configuration of the server where WatAA is deployed. Therefore, no `config.js` file is provided directly in the source code.
+
+Content of the `config.js` shall be as follows:
+
+    CONFIG={
+        server_url: https://wataa.somewhere.org,
+        update_year: 2015,
+        update_month: 5,
+        update_day: 9
+    };
+
+- `server_url`: URL on which WatAA is server
+- `update_year`: Year of the last update of the website content
+- `update_month`: Month of the last update of the website content (1 = Jan, 12 = Dec)
+- `update_day`: Day of the last update of the website content
+
+### Data
+
+This repository provides only WatAA source code. Data are distributed separately.
+
+Data files shall conform to the following naming scheme:
+
+#### PDB files
+
+PDB files shall be placed in a subdirectory named `pdbs`. Each file shall be named as follows:
+
+    {AMINOACID}_{SECONDARY-STRUCTURE}_{ROTAMER}.pdb
+
+- `AMINOACID` Three-letter aminoacid code, e.g. `ARG`
+- `SECONDARY-STRUCTURE` Either `H` or `E`
+- `ROTAMER` One of `g+`, `g-` or `t`. If there are no rotamers, `NA` shall be used instead
+
+##### Examples
+
+- ARG_E-g-.pdb
+- ALA_H_NA.pdb
+
+#### CCP4 density map files
+
+Density map files shall be placed in a subdirectory named `maps`. Each file shall be named as follows:
+
+    {AMINOACID}_{SECONDARY-STRUCTURE}_{ROTAMER}_clust0_water.map.ccp4
+
+Meaning of the variables is the same as for PDB files
+
+#### XYZ coordinate files
+
+Coordinate files shall be placed in a subdirectory named `xyzs`. Each file shall be named as follows:
+
+    {AMINOACID}_{SECONDARY-STRUCTURE}_{ROTAMER}_W{N}.xyz
+
+Meaning of the variables is the same as for PDB files. `N` variable is the number of the hydration site, starting from 1
+

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