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README
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README
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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.