Editing Bnitools (section)

== BNI Tools dropdown menu (Plugin > BNI Tools > ...) ==

     [+]Load Files->
      [-]modeller files
        * load multiple modeller files and sort by 
        * objective function energy 
        * and add energy to object title
      [-]autodock files
        * load autodock .dlg or .dlg.pdb file into
        * different states with energy in object 
        * title
      [-]amber minimization
        * load amber minimization file with energy in
        * title if the .info file is present in same
        * directory and has the same name as the pdb file.
      [-]delphi phi,dx map
        * load delphi map and corresponding pdb file
        * simultaneously and show surface colored by 
        * PHI or DX map. (show the surface to see the 
        *  effect)
      [-]casox map
        * load casox map (cavity calculation) and 
        * show ligsite accessibility 
        * value maps. (7 closed cavity to 1 open)
      [-]multiple files into states
        * load multiple pdb files (e.g. MD simulation 
        * snapshots) into one state. (object is named
        * by first object loaded)
     [+]Fetch->
      [-]Density View (EDS)
        * load density and pdb file from EDS
        * (Electron Density Server)
        * if available, and show density with density
        * wizard
      [-]RCSB Biol. Assembly
        * load biological assembly from RCSB
        * protein database
      [-]2FoFc map(s)
        * load (multiple) 2FoFc maps
        * from EDS density server
        * if available
      [-]FoFc maps(s)
        * load (multiple) FoFc maps
        * from EDS density server
        * if available
     [+]Edit->
      [-]HIS --> HID,HIE,HIP
        * change histidine residues to HID,HIE,HIP
        * depending on hydrogens on histidine
      [-]HID,HIE,HIP --> HIS
        * change altered histidine residues 
        * back to HIS
      [-]Poly-Alanine Chain
        * create a poly alanine chain (GLY and ALA)
        * for molecular replacement
      [-]MSE --> MET
        * change selenomethionine to methionine
      [-]del alternates
        * delete alternates in selection
      [-]Unbond- >
        * unbond atoms in selection
     [+]Images->
       * create ray traced images depending on
       * x size and resolution (dpi)
     [+]Create->
       * create compiled graphics objects (CGO)
       * these objects can be altered in color or
       * transparency, and they can be dragged
       * and rotated in space by the
       * "action->drag" command and using
       * "shift" and mouse buttons.
      [-]Plane
        * create a plane (with certain cushion)
        * using a selection of three atoms
      [-]Box
        * create a box around selection
        * the whole box can be altered as group
        * or by side planes separately
      [-]Triangle
        * create a triangle using a selection of three
        * atoms
     [+]pseudo center atom
         * create pseudo atom at the center of atoms
         * in selection
         * move atoms with editing->"shift"
         * and middle mouse button