Validate Entries Before Deposition


Depositors are encouraged to generate Validation Reports to monitor improvements made to structural models before deposition.

The RCSB PDB's Validation Server can be used to create validation reports outside of the deposition pipeline. Two options are available:

  • In the plain text report option, the server first checks the format consistency of the coordinates in the PRECHECK step. The precheck will produce a brief report identifying any changes that need to be made in your data files in order to obtain a validation report. In the validation step, the server produces an Atlas entry, a summary report, and a collection of structural diagnostics including bond distance and angle comparisons, torsion angle comparisons, base morphology comparisons (for nucleic acids), and molecular graphic images. Reports from PROCHECK1, NUCheck2, SFCheck3, and MolProbity4 are made available.
  • A new PDF report option produces a report that contains high-level geometric and experimental checking results without listing the detailed geometry. This unofficial report is similar to the wwPDB's PDF report generated during the annotation process for depositors to include with their journal submissions.

The Validation Server is available from the RCSB PDB Deposition Services page.

1 RA Laskowski, MW McArthur, DS Moss, JM Thornton (1993) J. Appl. Cryst. 265:283-291.
2 Z Feng, J Westbrook, HM Berman (1998) NUCheck. NDB-407 Rutgers University, New Brunswick, NJ.
3 AA Vaguine, J Richelle, SJ Wodak (1999) Acta Crystallogr. D55:191-205.
4 SC Lovell, IW Davis, BW Arendall, PIW de Bakker, JM Word, MG Prisant, JS Richardson, DC Richardson (2003) Protein Struct. Funct. Genet. 50:437-450.

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