Editing Bnitools (section)

== 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

[[Category:Plugins]]
[[Category:Pymol-script-repo]]