Difference between revisions of "Bnitools"

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|license  = BSD
 
|license  = BSD
 
}}
 
}}
= Template for a new page =
 
The following sections, can for example be copied to a new page.<br>
 
You can find tips for formatting a mediawiki page here: [http://www.mediawiki.org/wiki/Help:Formatting Help:Formatting]
 
  
== Introduction ==
+
[[File:bnitools.png||thumb|right|Screenshot of the BNI Tools plugin menu]]
A little section about what the script can do, and maybe why it has been developed and under which protein discipline it is particularly useful.<br>
 
Make the info box from [[Template:Infobox script-repo]].
 
  
=== Functions ===
+
'''BNI Tools''' is a plug in for PyMOL which adds additional functionalities and presets to the PyMOL GUI.
If there are more than one function, you could list them here.
 
* Make a dot
 
*: Write under same dot
 
  
== Example of use ==
+
== Installation ==
Here you can write a link to the protein in the example<br>
 
http://www.proteopedia.org/wiki/index.php/3ig7 <br>
 
  
Here you write some example of use. Try to make examples, that anyone can access right away.<br>
+
Install it using the 'Install Plugin' menu within PyMOL:<br>
Do this by fetching proteins, and if you need other example files, but them in: '''Pymol-script-repo/files_for_examples'''
+
'''PyMOL > Plugin > Plugin Manager'''<br>
<syntaxhighlight lang="python">
 
import colorbydisplacement
 
  
fetch 1HP1, async=0
+
== Example images created using BNI Tools ==
fetch 1HPU, async=0
+
[[File:bni_box.jpg|150px|||Create a box around a selection]]
+
[[File:bni_delphimap.jpg|150px|||Load and show DelPhi or other maps]]
hide everything
+
[[File:bni_box2.jpg|150px|||Create a box]]
### Select asymmetric units from pdb file
+
[[File:Bni_excludesurf.jpg|150px|||Exclude parts of surface]]
create O5NT, /1HP1//A
+
[[File:Bni_plane.jpg|150px|||Create Plane]]
create C5NT, /1HPU//C
+
[[File:Bni_track.jpg|150px|||Create a main chain track]]
delete 1HP1
+
== BNI Tools dropdown menu (Plugin > BNI Tools > ...) ==
delete 1HPU
 
 
show cartoon, O5NT
 
show cartoon, C5NT
 
  
ColorByDisplacementAll O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t
+
    [+]Load Files->
</syntaxhighlight>
+
      [-]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
  
== References ==
+
== BNI tools integrated in PyMOL sidebar ==
If you have used a particular article or figure to get inspiration to your script, then make a reference.
 
  
* ''Title of reference''. Author name. '''Journal name'''. Vol 08/12/2012, p. 54, fig. 5 [http://dx.doi.org/10.1016/0301-0104(89)87019-3  doi:10.1016/0301-0104(89)87019-3]
+
    [+]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:Plugins]]
 
[[Category:Pymol-script-repo]]
 
[[Category:Pymol-script-repo]]

Latest revision as of 10:45, 12 May 2016

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
Screenshot of the BNI Tools plugin menu

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

Installation

Install it using the 'Install Plugin' menu within PyMOL:
PyMOL > Plugin > Plugin Manager

Example images created using BNI Tools

Create a box around a selection Load and show DelPhi or other maps Create a box Exclude parts of surface Create Plane Create a main chain track

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

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