pdb_extract is an online tool which assembles specific details about your
experiment and experimental model from your coordinate and structure
determination output files in preparation for PDB deposition. This tool will:
- provide you with an author information form, which can be saved/updated for multiple related entries
- assemble coordinate and log files pertaining to your specific experimental methods
- allow you to "fix" the primary sequence of your protein/nucleotide chains to account for unresolved residues
- for X-ray structures, output the coordinate (and structure factor files, if applicable) in mmCIF format for
Validation and for
- for other method determined structures, output the coordinate (and structure factor files, if applicable) in mmCIF format for Validation and for deposition at RCSB ADIT or PDBj ADIT.
How to Run:
- Select your experimental method (X-ray, NMR or EM)
- Upload your fully refined coordinate file
- Select the file type and refinement program utilized
- Press the RUN button to start pdb_extract
- The mmCIF file(s) that you obtain should then be used as input for validation or deposition
- If the refinement program you used is not listed, select OTHER and write the name in the box provided.
- If the file size is large, it is recommended to upload gzipped (*.gz) or compressed (*.Z) file for faster loading.
Questions, comments, and suggestions should be sent to firstname.lastname@example.org.