Editing LiteMol:Hierarchy (section)

=Annotations=

This section describes entities which can store additional information about the structures, such as validation issues or sequence annotations.

==Validation Report (VR)==

[[File:LiteMol-validation_report.png | thumb | 250px | right| Structure of cytochrome P450 3A4 (1TQN) colored by the '''Validation Report''' from PDBe. ]]

[[File:LiteMol-ligand_validation_report.png | thumb | 250px | right| An oligosaccharide in the structure of ribosome-inactivating protein abrin-a (1ABR) colored by the '''Ligand Validation Report'''. The right-most residue is missing an atom. One of the residues in the center has an atom with which is the chirality. ]]

Represents geometric validation data for this molecule from the wwPDB validation report. The full validation report in PDF can be downloaded from the [http://www.ebi.ac.uk/pdbe/ PDBe site] (find your molecule, click ''Details'' in ''Experiments and Validation'' section, and then ''Full Validation Report'' in the right panel). An example of a validation report is available [http://www.ebi.ac.uk/pdbe/entry-files/download/1rtc_full_validation.pdf here].

Another type of '''Validation Report''' entity is '''Ligand Validation Report''', which represents validation data for the ligands in this structure. These data come from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB]. 

Applicable actions:
* '''Apply Coloring''' – The structure will be colored according the validation data. For '''PDBe Validation Report''' the color of each residue depends on the number of geometric outliers it contains: green = 0, yellow = 1, orange = 2, and red = 3 or more. For '''Ligand Validation Report''' the residues with missing atoms are colored in red. Also the atoms with wrong chirality are shown in red (examples can be found in PDB entry 1ABR). Correct residues are shown in green.


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==Sequence Annotations (SA)==

[[File:LiteMol-annotation.png | thumb | 250px | right| Structure of ricin A chain (4Q2V). The orange color indicates the part annotated as ''Ribosome-inactivating protein, subdomain 1'' by InterPro database. ]]

Represents a collection of sequence annotations via the  PDBe API, grouped by the source database.

==Sequence Annotation (SA)==

Represents a single sequence annotation, i.e. assignment of a name to a part of the structure. When you hover above this entity or click on it, the corresponding part of the structure will be shown in a distinctive color.

Applicable actions:
* '''Update PDBe Sequence Annotation''' – Allows you to change the color used for this part of the structure.


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