Parts of this section were taken from the Tuftsviewer wiki (courtesy of Matt Menke), located at the google code site that supports the source code.
Advanced Residue Selection
If "Xor Selection Rectangles" is selected in the Interface Menu, then when not pressing ctrl, the selection state of the residues in the selection rectangle is flipped. This means that dragging the selection rectangle over an area will deselect any selected residues and select any deselected residues.
Ctrl-A also serves to select all residues.
Ctrl-I inverts the current selection.
The Paths tab shows the locations of the local PDB and ASTRAL caches. If a local copy of either database already exists, just change the directory as needed to use it. Note that a number of file naming/location schemes are tried when searching for a local file (Compressed/uncompressed, single directory, or subdirectories using second and third letters of the PDB id, etc). In the URL, "%s" is replaced by the entire pdb or astral name, "%1" with the first character, "%2" with the second, etc. These codes do not work in the cache path fields.
The Display tab configures both how triangles are sent to OpenGL, the quality of the meshes that are used, the anti-aliasing level (if supported), and the dimensions of cartoons. Cartoon Quality is the number of slivers along the backbone while Cartoon Sliver Quality determines the number of triangles each sliver consists of. The cartoon for each residue uses roughly 8nm faces, where n is Cartoon Quality and m is Cartoon Sliver Quality. Spheres use roughly 12n^2 faces per sphere, where n is the Sphere Quality. Cylinders use 2n faces.
The first set of options set the rotation mode. In all modes, dragging around the window's edges rotates the structure. In Arcball
and Smoothed Arcball
, the rotation is uniquely determined by where the left mouse button was pressed and where it's released. Also, after rotating and releasing the mouse, clicking and dragging back to the original location restore the original location. In Arcball, the angle of rotation per pixel the cursor is moved is lower near the center than the edges, while in Smoothed Arcball it's roughly constant throughout. Direct only considers the current cursor position, and the position it was the last time the cursor position was read, so where the cursor is relative to the window makes no difference, except around the edges of the window.
The next set of options set the rotation center. In Absolute
mode, the model will always be rotated around the center of all atoms, regardless of whether or not they're visible or selection. In Visible
mode, the center of all visible atoms, if any, is used. If none are visible, the Absolute center is used. In Selected Visible mode, the center of all visible selected atoms, if any, is used. If no selected atoms are visible, it acts just like Visible mode.
Double Click to Unselect allows greater control by requiring a double click to deselect any selected residues.