Bnitools

Type	PyMOL Plugin
Download	plugins/bnitools.py
Author(s)	Georg Steinkellner
License	BSD
This code has been put under version control in the project Pymol-script-repo

Description

The bnitools is a plug in for PyMOL which adds additional functionalities and presets to the PyMOL GUI.

Installation

Linux and Windows

This plugin is distributed through the project Pymol-script-repo Install it using the 'Install Plugin' menu within PyMOL PyMOL > Plugin > Install Plugin

Functions

    # BNI tools dropdown menu 
    [+]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
  # BNI tools integrated in PyMOL sidebar
    [+]Action on "all"
     [-]delete enabled
       * delete all enabled objects or 
       * selections
     [-]invert enabled/disabled
       * disable currently enabled objects
     [-]combine selections
       * combine all enabled or disabled 
       * selections to selection (sele)
    [+]action
     [-]sequence
       * show sequence in different formats
       * of selection
       * copy and paste to text file for later use
       [.]fasta
         * show sequence of selection
         * in fasta format
       [.]pir
         * show sequence of selection
         * in pir format
       [.]modeller
         * show sequence of selection
         * in modeller pir format
       [.]list
         * create residue or atom lists
         * of selection
    [+]preset
     [-]track main chain
       * create a new object which tracks the
       * main chain atoms and shows main chain
       * and side chain polar contacts
     [-]symmetry surface
       * create a symmetry view of the selected
       * atoms showing the contact surface as well
       * as a selection entry of the atoms in 
       * contact with symmetry mates
       * (only includes atoms of the initial selection).
     [-]hydrophobic residues
       * show hydrophobic residues
       * depending on hydrophobic residue scales
       * by KandD (Kyte & Doolittle 
       *           J Mol Biol 157:105, 1982)
       *    Rose  (Rose et al. 
       *           Science, 229, 834-838,1985)
       *    GES   (Engelman Engelman et al. 
       *           Annu Rev Biophys Biophys Chem,
       *           15, 321-353(1986)
       * (no window selection; just raw categories
       * are colored by: blue-hydrophile
       *                green-neutral
       *                red-hydrophobe )
     [-]surface inspection
       * create selections for surface
       * inspections
  # BNI tools additional settings in PyMOL sidebar
     [+]color
      [-]by ss
        * color helix,sheet and loop separately
        [.]Helix
        [.]Sheet
        [.]Loop
      # this section is replaced by "[-] by_rep" in PyMOL versions >1.6
      [-]surface
        * color surface separately from atoms
        [.]by atom
          * set surface color to standard
        [.]by map
          * if a map or ramp is loaded
          * color surface by ramp/map
        [.]my color
          * color surface by own defined color
      [-]mesh
        * color mesh separately from atoms
        [.]by atom
          * set mesh color to standard
        [.]by map
          * if a map or ramp is loaded
          * color mesh by ramp/map
        [.]my color
          * color mesh by own defined color
      [-]label
        * color labels separately
        [.]by atom
          * set label color by atom
        [.]my color
          * color labels by own defined color
      [-]stick
        * color sticks separately
        [.]standard
          * set stick color to standard
        [.]my color
          * color sticks by own defined color
      [-]my colors
        * use/append own defined colors
        * own colors can be defined by
        * Setting->Colors..->New
        * to keep color settings for
        * other pymol sessions
        * you have to set the colors
        * in .pymolrc or similar
        * pymol setting file
        * like
        * set_color mycolor,[ 1.00, 1.00, 1.00]
     [+]show
      [-]surface flag
        * set surface flag of atoms to show hide
        * or ignore fro surface calculation
      [-]transparency
        * set different transparency types
        * on selections or atoms