validatordb: first time user guide

ValidatorDB

First Time User Guide

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PDB-wide validation statistics: reports about incomplete structures, incorrect chirality and chemical modifications.

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Would you like to see more details about validated molecules? Click here.

PDB-wide validation statistics: reports about incomplete structures, incorrect chirality and chemical modifications.

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Details by Molecule: Table summarizing validation results for individual ligands and non-standard residues

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Details by Molecule: Table summarizing validation results for individual ligands and non-standard residuesHover the mouse over the name of a category to see its description.

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Details by Molecule: Table summarizing validation results for individual ligands and non-standard residuesSort the table according to the results from the selected category.

7Add columns with additional categories of results.


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See results in percent's.

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Filter residues.

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See validation results for a selected residue.

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Molecule - MAN, Overview: Statistics of validation results for all MAN ligands in the PDB

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See summary of results.

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Molecule - MAN, Summary: Statistics of validation results for all MAN molecules in the PDB

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See detailed results.

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Molecule - MAN, Details: Detailed validation results for all MAN molecules in the PDB

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Select a subset of results.

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See results for a single instance of the residue.

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1E4M_16_4280 (MAN): Details about an individual molecule

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Select the visualization mode you prefer

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See superimposition of the validated and model molecule.

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See validation results for all ligands and non-standard residues in each PDB entry.

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Details by PDB Entry: Table summarizing validation results for individual PDB entries

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The table “Details by PDB Entry” can be operated with the same as the table “Details by Molecule”, i.e.: Sort according to the results of different categories, add columns with categories, see results in %.

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See validation results for a selected PDB Entry.

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PDB Entry – 3D12: Statistics of validation results for PDB entry 3D12

The validation results for the ligands and non-standard residues in PDB entry 3D12 are organized in a similar manner as for the previously discussed MAN molecule: summary of the validation report and detailed results.

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If you are looking for a specific molecule or a PDB entry you might want to try Search.

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Search: Select criterion for obtaining a validation report of specific entries or molecules

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Search: Select criterion for obtaining a validation report of specific entries or molecules

See examples of molecules and PDB entries, which exhibit errors either very commonly or very rarely. Detailed instructions about using the Search are also available.

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Samples: Examples of molecules and PDB entries, which exhibit errors either very commonly or very rarely.

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Samples: Examples of molecules and PDB entries, which exhibit errors either very commonly or very rarely.

See Step-by-step tutorials on how to use the ValidatorDB search functions.

validatordb: first time user guide

Science

detailed validation

pdbsee results

subset of results

man ligands

individual ligands

pdbsee detailed results

pdbsee summary of results

pdb13 molecule man