project-gemmi / periodic-table

Search PDB by elements.

Protein Data Bank entries by elements
A little utility made while testing the GEMMI library.

See: https://project-gemmi.github.io/periodic-table/

Author: Marcin Wojdyr
Copyright 2017 Global Phasing Ltd
License: Mozilla Public License 2.0


Update procedure
================

Update local copy of the mmCIF archive:

  REMOTE=rsync.ebi.ac.uk::pub/databases/pdb/data/structures/divided
  rsync -rlpt -v -z --delete $REMOTE/mmCIF/ /hdd/mmCIF

When choosing examples we consult with the Top8000 list:
  wget https://raw.githubusercontent.com/rlabduke/reference_data/master/Top8000/Top8000-SFbest_hom50_pdb_chain_list.csv

Go through the mmCIF archive and write down elements from each entry:

  ./make_elem_list.py /hdd/mmCIF/ > elems.txt

Update data.js (the number is the limit for number of PDB codes per one
element set):

  ./prepare_data_js.py elems.txt 15 > new-data.js
  mv new-data.js data.js

Update "Last update:" in html.