@*H BUT_C1(PhylogeneticTree) Displays a phylogenetic tree for a multiple sequence alignment and *@ @*H BUT_C1(ResidueSelection) Residue selections are objects attached to sequences which select one or more amino acid positions from the amino acid sequence. For example dragging the mouse in the alignment pane selects a continuous chain of residues which may be pasted e.g. into a BLAST web form. HTMLDOC_SEE_CLASS:BUT_C1(ResidueAnnotation) *@ @*H BUT_C1(View3d)

Menu-bar: If the user clicks inside the 3D-view, the menu-bar of the 3D-view and the 3D-tool bar are shown. In addition to this generic menu bar, 3D-programs may or may not have their own native menu bar which can be activated.

Undock menu items: Menu items like "spheres on" or "sticks on" which are frequently used can be dragged to the desktop with the mouse where they can be used directly without opening the menu first. Clicking "Spheres on" with the Shift key acts like "Spheres off".

Undock the viewer pane: 3D-views inside the Strap frame can be moved outside (undocking) which is most useful if there is a 2nd screen. For this purpose the head bar needs to be dragged with the mouse. Like all Strap windows, the undoked view can be set "Always floating on top of all other windows". Type Ctrl+T.

Picking an amino acid in the 3D-View: When atoms are clicked in the 3D-view, a toolbar with buttons that act upon the clicked amino acid appear.

Selecting amino acids in the alignment panel: Using the mouse or using Arrow keys together with Shift+← or Shift+→, a number of amino acids can be selected in Strap. This selection is passed to 3D. Alternatively, a residue selection can be dragged with the mouse into the 3D-view.

Adding proteins: Proteins can be added by WIKI:Drag_and_drop. See HTMLDOC_BUTTON:BUTS_MOVIE_Drag_to_another_STRAP!

Displaying Sequence Features: Sequence Features can highlighted in the 3D-view using WIKI:Drag_and_drop. See HTMLDOC_BUTTON:BUTS_MOVIE_Sequence_Features_in_3D!

3D-Superposition: 3D-Superposition allows to compare two or more protein backbones. Two options are available:
  1. All peptide chains in the view: One medium structure will be used as a reference. All other proteins are overlaid upon this reference peptide chain.
  2. All multi-chain complexes in the view: Different chains of the same PDB entry form a complex and their relative position is sustained. For superimposing two multi-chain complexes, the best structurally matching pair of chains is determined. I.E. for superimposing two trimeric G-proteins, the beta propeller structures may be selected. The superposition is computed for this pair of peptide chains and the transformation is applied to the entire complexes. Complexes might also be defined by the user or by a script - see context menu of proteins.
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