https://github.com/project-gemmi/pdb-stats
Clickable PDB statistics: synchrotrons and MX software
https://github.com/project-gemmi/pdb-stats
cross-filter pdb-files protein-data-bank statistics synchrotron x-ray-crystallography
Last synced: 6 months ago
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Clickable PDB statistics: synchrotrons and MX software
- Host: GitHub
- URL: https://github.com/project-gemmi/pdb-stats
- Owner: project-gemmi
- Created: 2017-10-24T18:12:39.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2025-03-07T19:42:06.000Z (7 months ago)
- Last Synced: 2025-03-27T09:45:27.734Z (7 months ago)
- Topics: cross-filter, pdb-files, protein-data-bank, statistics, synchrotron, x-ray-crystallography
- Language: JavaScript
- Homepage: https://project-gemmi.github.io/pdb-stats/
- Size: 7.68 MB
- Stars: 8
- Watchers: 3
- Forks: 4
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
These statistics serve as an example how to use `gemmi-grep`
(one of the utilities provided by the [project gemmi][1])
to quickly extract data from mmCIF files.
The data of interest is extracted from a local copy of the PDB archive
(mmCIF coordinate files) to a file `grep.out`:
$ ./extract.sh --auto
This script uses `gemmi-grep` to extract metadata to a file `grep.out`.
Reading all the archive (69GB of compressed files) takes about 30min.
The output is redirected to a file (`grep.out`) that is then used
to prepare JSON files used in our web pages.
### Filter-able statistics
`./process.py >data.json` makes a concise JSON file that includes only:
* entries deposited since 2008 (aribitrary cut-off),
* obtained using X-ray crystallography,
* in case of group depositions (PDB has now only a dozen of such groups)
we take one entry from each group.
The web app itself is contained in a single file (index.html).
It depends on three external libraries: dc.js, d3.js and crossfilter.
Here is an interactive demo (each plot can be used as a filter):
https://project-gemmi.github.io/pdb-stats/
### Synchrotron work patterns
`./coldates.py` prepares json files for calendar.html, see `extract.sh`.
https://project-gemmi.github.io/pdb-stats/calendar.html
### Residue statistics
$ curl -O ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
$ ./resistat.py $PDB_DIR/structures/divided/mmCIF > residues.json
$ # update file_count and date in residues.html (take file_count from json)
https://project-gemmi.github.io/pdb-stats/residues.html
### Tag statistics
File entries.idx is used to sort entries from the most recent ones,
so that the example PDB ID in tooltip is the newest entry with given tag.
$ curl -O https://files.wwpdb.org/pub/pdb/derived_data/index/entries.idx
$ gemmi tags --full components.cif.gz > ccd-tags.tsv
$ gemmi tags --full --entries-idx=entries.idx $PDB_DIR/structures/divided/mmCIF > mmcif-tags.tsv
$ gemmi tags --full --entries-idx=entries.idx --sf $PDB_DIR/structures/divided/structure_factors > sf-tags.tsv
$ sed -i s"/ on 20..-..-../ on $(date -Idate)/" tags.html
https://project-gemmi.github.io/pdb-stats/tags.html
Similarly, for the COD:
$ gemmi tags --full path/to/cod/cif/ > cod-cif-tags.tsv
$ gemmi tags --full --glob='*.hkl' path/to/cod/hkl/ > cod-hkl-tags.tsv
$ sed -i s"/ on 20..-..-../ on $(date -Idate)/" cod-tags.html
https://project-gemmi.github.io/pdb-stats/cod-tags.html
[1]: https://project-gemmi.github.io/