Editing ValidatorDB:Analysis of Results (section)

==Complete structures==
[[File:VDB chirality.png|thumb|right|500px| Complete structures can contain chirality issues on a variety of different atom types, here all possible cases occuring in '''ValidatorDB''' are illustrated.]]

Complete validated structures include all the atoms which are present in the model residue. However, there are still possible issues and warnings can be raised:

* '''Wrong chirality''': an atom from the validated motif has different chirality than the corresponding atom from the model residue. This category can be further specified by identifying a source of the chirality issue.
** '''C atom''': the chirality error was found on a single bonded carbon atom.
** '''Planar atom''': the chirality error was found on a planar chiral center. Because of their spacial distribution, planar chiral centers are very sensitive even to small perturbations in the position of the substituents. Therefore, some of the errors reported here might not be significant.
** '''Metal atom''': the chirality error was found on a metal chiral center. 
** '''High order atom''': the chirality error was detected on an atom, which is bonded with a bond of higher order than one. A typical example is phosphorus. 
** '''Other''': Additional chirality issue which could not be asserted to any of the above categories, for example chirality issues on Nitrogen.







Note that in case a validated residues belongs to more than one category, it can be found in all of them (i.e. Planar and Metal, which is often case of ''HEM'' residues)

* '''Uncertain chirality''': the presence of unusual bonds may cause an improper evaluation of chirality.
* '''Substitution''': An atom from the validated motif is of a different chemical element than the corresponding atom in the model residue (e.g. O mapped to N). This happens often at linkage sites.
* '''Different naming''': An atom from the validated motif has a different PDB atom name than the corresponding atom from the model residue (e.g. the C1 atom mapped to the C7 atom). This happens often when the original PDB files were produced by different software.
* '''Foreign atom''': An atom from the model residue was mapped to an atom from outside the validated residue (i.e. from its surroundings).
* '''Alternate conformations''': In the original PDB file, the validated residue contains atoms which were given in conformations (i.e., most probably different rotamers). Only the first rotamer was considered during validation.
* '''Zero model RMSD''': The superimposition between the model residue and the validated motif has a root mean square deviation of zero, i.e., the validated motif is identical to the model residue used as reference.

The last category  '''Correct chirality''' includes all the validated residues, where all the atoms from the validated motif have a matching partner in the model structure and the chirality of the chiral atoms is correct. Last but not least, additional category '''Correct (Tolerant) chirality''' further includes motifs with identified chirality issues as '''Planar''' and '''High order''' since these might not be significant.

Furthermore, for each validation run, there is '''Processing warnings''' tab available, where one can find warnings about the processed structures. Typically, there is an information about skipped ''alternate  conformation residues'', ''wrong CONNECT records'' from the parent PDB file, ''processed models'' (in case the parent PDB is composed of multiple models) etc. Finally, as a general rule, in the validation interface, errors are marked in <span style="color:#FF0000">red</span> (missing atoms) or <span style="color:#DAA520">dark yellow</span> (wrong chirality), correct structures in <span style="color:#228B22">green</span>, and warnings in <span style="color:#008B8B">cyan</span>.

[[File:VDB warnings.png|thumb|left|1000px| '''ValidatorDB''' also reports warnings in the complete structures such as ''substitutions'', ''different naming'' or ''foreign atoms''.]]