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BALLView Documentation

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Structure Window

The structure window gives a hierarchical overview of the loaded molecules and provides means to interact with the molecular entities.



Every molecule is part of a system, molecules from different systems do not interfere with each other, e.g. in MD-Simulations. BALLView creates a new System for every molecular file, the user loads.

Highlighting

By clicking with the left mouse button on the names of molecular entities, users can highlight these. To highlight more then one item, use the Shift- or Control-modifier. A click with the right mouse button will open a context menu, which will operate on the highlighted molecular items:

Selections (or how to find an atom)

Left of the names of the molecular entities are checkboxes, which show the user which molecular entities are currently selected (picked). The selected objects become colored in the 3D view. This can be used to find an atom in the three-dimensional structure of its molecule. If a user starts a molecular dynamics simulation or an energy minimization while some molecular entities are selected, BALLView only operates on these items (which is e.g. useful for optimizing the position of only the hydrogen atoms of a protein from a PDB-file).

Cut, Copy, Paste

The user can cut or copy any molecular entities in the Molecular Control and also paste them into other objects (see the Menu point "Edit"). This makes it possible e.g. to merge Systems:
  1. Load two molecular files (e.g. PDB files)
  2. Highlight the molecules of the first System (they should become blue like in the picture above)
  3. Click on the menu entry "Cut" in "Edit"
  4. Highlight the second System
  5. Click on the menu entry "Paste" in "Edit"
  6. The first System can now be deleted

Regular expressions

At the bottom of the Molecular Control resides a text field. In this text field, the user can enter expressions to select molecular entities. To apply the typed expression, either press the Return key or the "Select" button. The "Clear" button clears the current selection. Possible predicates are:

true() always true
false() always false
SMARTS(string) use a SMARTS expression
selected() true for already selected atoms
name(string) the name of an atom
type(string) type name of an atom
element(char) element (abbreviated by its symbol)
residue(string) name of a residue
residueID(string) PDB ID of the residue (usually a number)
protein(string) name of protein, the atom is contained in
secondaryStruct(string) name of the secondary structure, the atom is contained in
chain(string) name of the chain, the atom is contained in
nucleotide(string) name of the nucleotide the atom is contained in
solvent() the atom is a solvent atom added by BALL
backbone() backbone atoms
inRing() part of a ring
doubleBonds() atoms with double bonds
tripleBonds() atoms with triple bonds
numberOfBonds(int) atoms with a given number of bonds
aromaticBonds() atoms with aromatic bonds
connectedTo(char) atoms which are connected to an atom (see ConnectedTo Predicate in the BALL documentation)
charge([op][number]) select by charge, Possible operators are '<'  '<='  '='  '>='  '>'
spHybridized()  
sp2Hybridized()  
sp3Hybridized()  
charge(float) atoms with given charge
isAxial()  
is4C1()  

All predicates can be connected with AND and OR, grouped with brackets, and each predicate can be negated with '!'
Example:   !residueID(12) AND (element(N) OR element(C))

Properties of Molecular Entities

To view and modify the properties of molecular entities, BALLView offers a special dialog, which can be opened in the context menu of the structure window under the point "Properties". In this dialog the user can e.g. set the name of a chain or change the charge of atoms. (Another fast way to obtain the basic information for an atom, is to select (pick) exactly one atoms. The information like charge and position are then shown in the logs window.)



Another dialog enables the user to obtain all information of any bond. To open this dialog, one atom has to be highlighted and the context menu entry "Show Bonds" has to be clicked. In this dialog, the user can read the bonds order and type. The "Select" buttons in the dialog enable the user to identify the partner atoms in the bond.

Distances and angles between atoms

When exactly two atoms are selected (picked) the distance between them is shown in the logs window and the status bar. For three selected atoms, the angle between them is shown, and for four atoms the torsion angle.

Count atoms and bonds

The context menu also has an entry to count the bonds and atoms of the currently selected molecular entity (e.g. a Residue).

Move molecular entities

To move parts of structures or individual atoms, the user can highlight them and switch to a special move mode with the context menu entry "Edit->Move". The mouse cursor changes to indicate the new mode. In this mode the mouse can be used to move and rotate all selected items. This works the same way as the normal rotation and translation of the viewpoint. To switch back to the rotation mode, the user can press either the Escape key or click on the menu entry "Display->Rotate Mode" .

Selection and Highlighting

The selection and the highlighting can be converted into each other through the context menu. To select highlighted items use "Select", selected items can become highlighted by pressing "Highlight Selection". This is e.g useful for creating a Representation for picked molecular items or for finding a picked atom in the hierarchical overview in the structure window (the parent entries of the selected objects will be opened).

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Created by anhi
Last modified 2007-11-01 08:26 PM