Atomic Detail: Shows everything in atomic detail with Ball & Stick representation.Smaller structures are shown with more detail than larger ones, ranging from atomistic display to coarse surfaces. Automatic: Chooses a Basic preset based on the size (residue count, number of symmetric chains) of a structure.Empty: Removes all representation to give you a blank slate to work with.The following are the presets available and a description of their functions. The components shown depend on the structure and what preset is chosen as well as what components are created. Additional components can be added by selecting groups of atoms, residues, or chains. For more information, see Components Logic.īy default, the preset that shows up when a structure is Polymer & Ligand, in which the polymers, ligands and water components are shown. Components are representations of certain parts of the structure being visualized. The Components Panel shows options for the manipulation and display of the contents of the structure(s) being viewed. The icons in the Dihedrals menu perform the same actions as those in the Labels menu. Additionally, the options button next to the Add button gives the option to change the units in which distance is measured, as well as color options for the text display on the 3D canvas. This allows the user to make all of their selections first and then specifying which of the selections should be used for the measurements (toggling them up to the top of the selections listing). Within the Measurements Panel, the selections can be toggled up and down using arrows that show up next to them. This means that if three residues are selected for an angle measurement, the angle will not be taken from the alpha carbon, but from a point from the center of the space the residue takes up. If another Picking Level, such as residues or chains, is used, the measurements will be made using points from the center of the space that the selection occupies. When the selections are atoms, the measurements will be made from the center of the atoms. The measurement will be made based on which Picking Level is used for the selections. See Selection Mode for information on making selections. Without the appropriate number of selections, the measurement options will not be available for use.
In order to take measurements, the appropriate number of selections need to be made - two selections to measure distance, three selections to measure angles, and four selections to measure dihedrals. To start making measurements, click on the Add button and a drop-down menu will show up.
The Measurements Panel allows the user to make desired measurements in a structure ( labels, distance, angles, dihedrals) to observe relationships between units in the structure (e.g. Biologically Interesting Molecule Reference Dictionary (BIRD).
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