Editing LiteMol:Hierarchy (section)

==Root Entity==

The highest level of the hierarchy is the '''Root Entity''', which is created at the beginning of LiteMol session. It represents the starting point of all actions and all other entities you create are its direct or indirect descendants.

Applicable actions:
* '''Molecule''' – Loads a structure of a molecule and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. The structure can be obtained from several sources:
** '''CoordinateServer''' - Downloads the structure from an internet location that provides [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] functionality. These parameters can be set: 
*** '''Id''' - Specify the PDB identifier of the structure.
*** '''Type''' - Can be either '''Full''' (coordinates of all atoms are downloaded) or '''Cartoon''' (only atoms necessary for cartoon visualization are downloaded, so the download will be faster).
*** '''Low Precision''' - If '''Low Precision''' = Off, the atomic coordinates are downloaded in full precision (3 decimal places). If '''Low Precision''' = On, then the coordinates are downloaded only with 1 decimal place. This change is almost unnoticeable in the visualized structure but less data are downloaded.
*** '''Server''' - By default, the data are downloaded from the CoordinateServer located at webchem.ncbr.muni.cz/CoordinateServer, however, this can be changed.
** '''PDBe Updated mmCIF''' - Downloads the structure from the PDBe server (e.g. www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif) using the updated mmCIF format file. 
** '''URL''' - Downloads the structure from any specified internet location.
** '''File on Disk''' - Loads the structure from a file on your computer. The format of the file will be inferred from its extension.
* '''Density Data from PDBe''' – Downloads the electron density or electronic potential map for a molecule specified by its PDB ID (or EMDB ID) from the PDBe server and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. However, a much faster way to visualize densities is to create a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and then use the '''Density Streaming''' action. 
* '''Coordinate Streaming''' – Downloads the portion of structural data that is necessary for simple visualization of a molecule. If more data are needed later, they will be downloaded automatically. This behavior is particularly useful when working with extremely large molecules, where full download may take more time, or when limited by hardware resources (slow/expensive Internet connection, limited memory) especially on mobile devices. You can specify what server should be used as the source of the data (e.g. http://webchemdev.ncbr.muni.cz/CoordinateServer or http://www.ebi.ac.uk/pdbe/coordinates). Creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity.
* '''Download Data''' - Acquires a data file from a URL. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.
* '''Open Data File''' - Loads a data file from your computer. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.