Editing LiteMol:Hierarchy (section)

==Molecule Model (M<sub>M</sub>)==

[[File:LiteMol-default.png | thumb | 400px | right| Model of the protein with PDB identifier 1CBS in default visualization produced by '''Macromolecule Visual''' ('''Cartoon''' for biopolymer, '''Balls and Sticks''' for non-biopolymer ligand, and '''Balls and sticks''' with '''Opacity''' 0.25 for water molecules). ]]

A '''Molecule Model''' entity represents a static model of a molecule, i.e. 3D coordinates of each atom. (If your PDB entry contains multiple alternative models, each of them will be in a separate '''Molecule Model''' entity.)

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Assembly''' – Some PDB entries contain information about how multiple copies of the molecule should be positioned in space in order to create an assembly (e.g. a virus capsid). Alternatively,  just a part of the model can constitute a relevant assembly (e.g. the model contains a two molecules while a monomer is present ''in vivo''). This action applies this information to your model and creates a new model containing the assembly. Some PDB entries provide more than one assembly.
* '''Crystal Symmetry''' – Creates a new model containing the original molecule and its closest neighbours in the crystal structure. Two modes are available: '''Interaction''' shows only those atoms that are within the specified radius (in Angstrom) from the original structure, '''Mates''' shows all copies of the structure that have at least one atom within this radius. This action is obviously not available for structures determined by NMR.
* '''Macromolecule Visual''' – Creates a visual representation of the model. If the model contains several types of molecules (e.g. protein + ligand), these are organized in a group of selections and appropriate visualization is used for each selection (e.g. '''Cartoon''' for protein but '''Balls and sticks''' for ligand). The same visuals are created automatically when the '''Molecule Model''' entity is created.
* '''Visual''' – Creates a visual representation of the model. This option is less automatic than '''Macromolecule Visual''' but more flexible. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Coordinate Streaming''' – Works in a similar way as '''Coordinate Streaming''' from the [[LiteMol:Hierarchy#Root Entity | Root Entity]]. If you click on an atom or residue, the coordinates of all atoms in the surrounding volume will be downloaded instantly. This can be useful when a part of the structure has already been downloaded (e.g. the protein backbone) and some additional atoms are required (e.g. sidechains to display the binding site).
* '''Update Model''' – Applicable when multiple models are included in the PDB entry (typical case for NMR structures). This action will remove the current model and create a new model with the specified index (model number). Please keep in mind that this will remove all the changes you have applied to the current model! If you don't want to loose these changes, go to the superior [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and create a new model in addition to the current model.


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