Editing LiteMol:Hierarchy (section)

=Visualization=

This section contains entities that represent different visualizations of molecules and electron density maps.

==Molecule Visual (V<sub>M</sub>)==

[[File:LiteMol-cartoon.png | thumb | 250px | right| '''Cartoon''' visual for 1CBS. ]]

[[File:LiteMol-CA_trace.png | thumb | 250px | right| '''C-α trace''' visual for 1CBS. ]]

[[File:LiteMol-balls_and_sticks.png | thumb | 250px | right| '''Balls and Sticks''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-VDW_balls.png | thumb | 250px | right| '''VDW Balls''' visual for 1CBS colored by '''Element Symbol'''. ]]

[[File:LiteMol-surface.png | thumb | 250px | right| '''Surface''' visual for 1CBS. ]]

A '''Molecule Visual''' is simply a visualization of a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] or its part. It is defined mostly by its type and coloring. These can be changed in '''Update Visual''' action. Click on the “+” icon next to “Type” or “Coloring” to modify other attributes. Some attributes are only available for certain types of visualization.

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]].
* '''Update Visual''' – Allows you to change the type of visualization and other attributes.

List of attributes:
* '''Type''' – One of the following:
** '''Cartoon''' – Schematic representation of the backbone with distinction of helices, strands, and unstructured regions.
** '''C-α Trace''' – Simplified wire-like representation of the backbone (no side-chains).
** '''Balls and Sticks''' – Atoms are represented by balls, bonds are shown as sticks connecting them. Keep in mind that most structures from X-ray and cryo-EM experiments do not provide positions of hydrogen atoms, so these are not visible in '''Ball and Sticks''' representation. There are some extra attributes that you can modify:
*** '''VDW''' – Indicates whether all atoms are shown as spheres with uniform radius ('''VDW''' = Off) or the radius of the sphere radius is based on the element's Van der Waals radius ('''VDW''' = On).
*** '''Scale''' – (Only when '''VDW''' = On) The ratio between the sphere radius and the element's Van der Waals radius.
*** '''Atom Rds''' – (Only when '''VDW''' = Off) The radius of the sphere in Angstrom. 
*** '''Bond Rds''' – The width (radius) of the sticks.
*** '''Bond''' – Color of the sticks. 
** '''VDW Balls''' – Shows atoms as spheres width radii corresponding to their Van der Waals radii.
** '''Surface''' – Shows the smoothed boundary surface of the space “filled” by the molecule. There are some extra attributes that you can modify:
*** '''Probe Radius''' – How much space around an atom is considered as “filled” by this atom.
*** '''Smoothing''' – With lower values, curvature of the surface around individual atoms will be more noticeable. With higher values the surface will be smoother.
*** '''Auto Detail''' - If set to On, the optimal level of detail is automatically derived from the size of the molecule. If set to Off, the level of detail can be adjusted manually (see the next item).
*** '''Detail''' – Defines precisely how the surface should be visualized. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource demanding) when visualizing larger molecules.
*** '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).
* '''Detail''' – Defines how precisely the molecule should be visualized and can range from '''Very Low''' to '''Very High'''. While higher detail provides nicer pictures for small molecules, lower detail is a better option (faster and less resource demanding) when visualizing larger molecules. If you choose '''Automatic''', LiteMol will infer the optimal level of detail from the molecule's size.
* '''Coloring''' – One of the following:
** '''Chain ID''' – Every chain will be shown in a different color.
** '''Entity ID''' – The same as '''Chain ID''' but chemically identical chains are shown in the same color.
** '''Entity Type''' – Every type of entity (polymer, non-polymer, water) is shown in a different color.
** '''Residue Name''' – A different color is used for each type of residue.
** '''Element Symbol''' – A different color is used for each element.
** '''Rainbow (Chain)''' - Colors each chain in the colors of rainbow from N-terminus (red) to C-terminus (violet) (or from 5' to 3' in nucleic acids).
** '''Rainbow (Entity)''' - Similar to '''Rainbow (Chain)''', but chemically identical chains are treated as a single longer chain (e.g. in a homodimer).
** '''Uniform Color''' – One selected color is used for the whole '''Visual'''.
* '''Highlight''' – The color in which this '''Visual''' will be temporarily colored when hovering over the '''Visual''' entity in the entity tree. When the cursor is placed on an atom or residue, it will be colored in the same way.
* '''Selection''' – If you create a [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] from this '''Visual''', it will be distinguished from the rest of the '''Visual''' by having this color.
* '''Opacity''' – The level of transparency of the '''Visual'''. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).

Please keep in mind that changing the type of a '''Visual''' will in fact remove the current visual and replace it with a new one, so all changes you have applied to the current '''Visual''' (such as creating a selection from it) will be lost! You can go to the superior entity and create a new '''Visual''' besides the current '''Visual'''.


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==Density Visual (V<sub>DD</sub>)==

[[File:LiteMol-density_visual.png | thumb | 250px | right| Density isosurface at 1.5 σ (2Fo-Fc). ]]

Represents an isosurface of electron density, i.e. the surface in 3D connecting all the points with the value of electron density equal to a specified isovalue.

Applicable actions:
* '''Update Surface''' – Allows you to change the attributes of the visualization.

List of attributes:
* '''Iso value''' – The isovalue of electron density used for the visualized surface.
* '''Relative''' - Indicates whether normalized ('''Relative''' = On) or unnormalized ('''Relative''' = Off) density values are used. The relationship between the two values is as follows: ''Normalized'' = (''Unnormalized'' - ''Mean'') / ''Sigma''.
* '''Color''' – The color of the surface.
* '''Opacity''' – The level of transparency of the surface. The value 1 means totally opaque whereas the value 0 means totally transparent (thus invisible).
* '''Wireframe''' – Toggles between visualization as a solid surface ('''Wireframe''' = Off) and a transparent wire-like representation ('''Wireframe''' = On).


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==Interactive Surface (B<sub>IS</sub>)==

[[File:LiteMol-interactive_surface.png | thumb | 250px | right| Interactive density isosurface at 1.5 σ (2Fo-Fc) shown for a tryptophan residue and its surroundings with radius 2 Angstroms. ]]

This is a visualization of an isosurface of electron density, just as [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]]. The difference is that this surface is shown only when you click on a residue or an atom in the structure. The surface is shown only for the region around the selected residue or atom. An advantage of this interactive visualization is that the relevant region of density surface is not hindered by the rest of the molecule.

Three default '''Interactive Surfaces''' are created automatically when loading density data: blue surface corresponds to isovalue 1.5 in 2Fo-Fc density map. Green and red surfaces correspond to isovalues +3 and -3 in Fo-Fc difference density maps.

Applicable actions:
* '''Update Interactive Surface''' – Change the attributes of the visualization. These attributes are the same as in the case of [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity. An extra attribute is '''Radius''', which allows you to change the size of the region for which the isosurface is shown. Attribute '''Show''' toggles between interactive visualization around the selected region ('''Show''' = Around Selection) and static visualization of the whole map ('''Show''' = Everything, practically equivalent to [[LiteMol:Hierarchy#Density Visual (VDD) | Density Visual]] entity).


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