{"id":296,"date":"2019-07-12T17:03:56","date_gmt":"2019-07-12T17:03:56","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/mgltools\/?page_id=296"},"modified":"2019-07-12T17:40:22","modified_gmt":"2019-07-12T17:40:22","slug":"doc-156-dashboard","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/mgltools\/doc-156-dashboard\/","title":{"rendered":"doc 156 dashboard"},"content":{"rendered":"

Dashboard<\/h2>\n

With Pmv 1.5.6 we introduce a completely re-designed dashboard widget that facilitates carrying out Pmv commands that previously required navigating through several menus and forms with a single click. This interface presents molecules and molecular fragments in a tree structure. The matrix of buttons to the right of the tree is used to carry out the Pmv command corresponding to the column on the molecular fragment corresponding to the line. For instance, in the picture below, the crosshair is on the \u2018S\u2019 column which is the Pmv selection command and the chain \u2018B\u2019 line under protease, a protein loaded in Pmv. As the tooltip indicates, clicking a first time on this square button will select the chain B of protease. Clicking a second time on this button will deselect the entire protein.<\/p>\n

\"Macintosh<\/p>\n

The Pmv commands mapped to the columns of buttons are: select \"Macintosh , display lines \"Macintosh , display balls and sticks \"Macintosh , display CPK \"Macintosh , display Ribbon \"Macintosh , display molecular surface \"Macintosh , display labels \"Macintosh , and color \"Macintosh commands. Tooltips indicate the function of each button.<\/p>\n

There are three types of buttons in the Dashboard. The first type \"Macintosh is a stateless button with 2 functions: the green circle carries out the command (i.e. select, display, label) while the red circle negates the command (i.e. deselect, undisplay, unlabel).<\/p>\n

The second type of buttons (e.g. \"Macintosh , \"Macintosh , \"Macintosh \"Macintosh , \"Macintosh ) the fraction of the group for which the state is on. In the picture above, all of protease is displayed as lines so there are full solid red circles in the display line column, while only chain A is displayed as balls and sticks so the circle for chain A displayed as balls and sticks is solid while the circle for balls and sticks for protease is \u00bd solid (i.e. 1 chain out of 2). Clicking on a button that has less than 100% of its children on forces the command on all children. Clicking on a button that is completely on (solid) negates the command. In other words, the cycle is \"Macintosh => \"Macintosh => \"Macintosh => \"Macintosh \u2026 where => represents clicking on the button.<\/p>\n

In general, left clicking on a button carries out the command with default parameters, while right click opens an option panel specific to the command. However, there are exceptions. For instance, the menu buttons for labeling and coloring have no action associated with the right click event while the selection command has a selection menu associated with the right click.<\/p>\n

Molecular Fragment menu:<\/h3>\n

Right clicking in a molecular fragment in the tree widget will bring up a menu that will vary based on the fragment. For instance, right clicking on \u201cPmv Molecules\u201d triggers the read molecule command that displays a file browser for selecting a molecular file to read. Right clicking in \u201cCurrent Selection\u201d offers the options: to split the selection (i.e. make the current selection a different molecule) or to show the selection in the 3D Viewer by translating and scaling the scene. Right clicking on a molecule displays a longer menu with options to delete the molecule, view the text file from which the molecule was read, etc\u2026<\/p>\n

Working with the \u2018Current Selection\u2019:<\/h3>\n

Pmv has powerful commands for creating selections. In the dashboard, one can type selection strings \"Macintosh to create a selection or use the button in the left most column \"Macintosh . The line of buttons located to the right of \u2018Current Selection in the tree \"Macintosh supports operations on the current selection. Note that there is no button on in the Select column of that line, since selecting the current selection does not do anything.<\/p>\n

Creating custom sets:<\/h3>\n

A Pmv selection can be saved as a new line in the Dashboard to facilitate rapid Dashboard-based operations on this specific subset. This is done using the \"Macintosh button in the upper left corner. When this button is clicked on and there is a selection, a dialog is displayed asking for a name\u00a0for the set.\"MacintoshClicking \u2018OK\u2019 in this dialog will add a line to the dashboard tree widget \"Macintosh .<\/p>\n

Sets can be renamed or removed through the menu obtained by right clicking on the set name in the tree widget.<\/p>\n

Configuring the Dashboard:<\/h3>\n

The button located above the tree widget sets the dashboard width so that all command columns are visible ( \"Macintosh ), increases the size of the command button ( \"Macintosh ), and decreases the size of the command buttons ( \"Macintosh ). Note that the height of the lines in the tree is fixed, which causes the circles to become ovals for large button sizes.<\/p>\n

The selection command menu:<\/h3>\n

\":::::Desktop:Screen This menu is obtained by right clicking on the buttons in the select command column. It allows the user to tailor the selection by specifying groups of atoms to add or remove form the selection. By default, atoms are added to the selection. To Remove parts of the selection the first check the \u2018Deselect\u2019 button then specify the atom set using the next five entries, which are shortcuts for selecting common subsets of atoms. Here, Hetero Atoms<\/strong> are the atoms from HETATM records in PDB files.<\/p>\n

The following 6 sets are predefined as follows:<\/p>\n