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Using the CCPN XML files from DOCR/FRED/RECOORD
A short guide on the steps that you have to take to use this data
- Download and install the CCPN software. If you just want to run scripts on the data, the API release is sufficient. If you want to export the data into other formats, you need the FormatConverter release. If you also want to look at the structures and constraints inside the data model, you need the Analysis release.
- Download the CCPN XML files. There are currently 2 places where you can download (different) data:
- RECOORD data: Information for over 500 monomer PDB entries with NMR constraints. These files include the original coordinates and restraint lists, as well as the 'cleaned' restraint lists and the coordinates for the structures recalculated using these lists (CNS, CNS water refined, CYANA, CYANA water refined).
- Go to the MSD home page.
- Enter the PDB code for the entry you want in the top right 'Get PDB by ID' window, and press enter.
- If there is NMR information available, you will see an 'NMR data' link on the left-hand side. Click this.
- If RECOORD data is available, you will see a relevant RECOORD information row in the NMR data window. Click on the 'CCPN files' link in the 'Download' row to get a gzipped tar archive of the CCPN project.
- Unpack the archive (using 'tar xvfz <file>.tgz' in a Unix/Linux type environment).
- Note that you can also browse the RECOORD data.
- DOCR/FRED data: Information for almost 3000 PDB entries with NMR constraints. These files only include the original coordinates, the original restraint lists and 'cleaned' restraint lists (by the Wattos program).
- Go to the BMRB NMR restraints grid home page.
- Type the PDB (or BMRB) ID at the top, press enter.
- If any results were found, click on the 'Total' link (top right of table).
- Click on the link in the mrblock_id column in the column that contains 4-filtered-FRED and XML.
- Download the results by clicking on the symbol next to '(Save to zip file containing files for each block)'.
- Unzip the downloaded query.
- Unpack the block_####.tgz archive file (using 'tar xvfz <file>.tgz' in a Unix/Linux type environment).
- You now have the relevant entry, and can load the information with the FormatConverter or Analysis, or run any of the scripts provided here.
Ph.D. in protein NMR spectroscopy
CCPN General Meeting