Validation Server Tutorial

The RCSB Validation Server allows the user to check the format of coordinate and structure factor
files and to create a variety of validation reports about a structure. These checks are completed independently by the user.

Structures can be deposited using the AutoDep Input Tool (ADIT).

Using the ADIT Validation Server:

We encourage all depositors to compress their files in .gzip or .Z format, as this will speed up the file upload and validation process.

  1. From the pull-down menus provided, select the experimental method and press the BEGIN button. This will bring you to a new Web page.
  2. Enter the path/location of the coordinate file and structure factor file (if applicable) in the space provided. You may also select the Browse button to locate the files.
  3. Specify the coordinate file type (PDB or mmCIF) and structure factor file type (mmCIF or Other). Currently, the validation reports for structure factor files can only be created for files submitted in mmCIF format.
  4. Select the operation you wish to perform (precheck or validate) and then press the BEGIN button.

You will be presented with either a Precheck summary report or a Validation summary report.

Coordinate Format Check

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.

For validation, the coordinate file must be in either PDB or mmCIF format, and must include: a complete CRYST card (unit cell and space group information), chain IDs, and TER cards at the end of each chain. Scale cards must be provided if an alternate setting is being used for space group symmetry.

After the precheck has been successfully completed, you may press continue to proceed to the next page. Select validation from the operation menu, and then press BEGIN to create the Validation report.

Validation

The validation may take a few minutes depending on the size of your structure, so please be patient.

If atom names or HETATM residue names are unrecognized by the dictionaries, validation results will not be optimal. If you wish to send us the definition for any new HETATM groups we will include them in our dictionaries. New HETATM groups can be sent to deposit@deposit.rcsb.org or faxed to 732 445 4320.

When the validation process is complete, you will be presented with a validation report which includes 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.

Questions, comments, and suggestions should be sent to deposit@deposit.rcsb.org.