Difference between revisions of "Bnitools"
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{{Infobox script-repo | {{Infobox script-repo | ||
|type = plugin | |type = plugin | ||
− | |filename = | + | |filename = plugins/bnitools.py |
− | |author = [[User: | + | |author = [[User:Steinkeg|Georg Steinkellner]] |
|license = BSD | |license = BSD | ||
}} | }} | ||
+ | |||
+ | [[File:bnitools.png||thumb|right|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:<br> | ||
+ | '''PyMOL > Plugin > Plugin Manager'''<br> | ||
+ | |||
+ | == Example images created using BNI Tools == | ||
+ | [[File:bni_box.jpg|150px|||Create a box around a selection]] | ||
+ | [[File:bni_delphimap.jpg|150px|||Load and show DelPhi or other maps]] | ||
+ | [[File:bni_box2.jpg|150px|||Create a box]] | ||
+ | [[File:Bni_excludesurf.jpg|150px|||Exclude parts of surface]] | ||
+ | [[File:Bni_plane.jpg|150px|||Create Plane]] | ||
+ | [[File:Bni_track.jpg|150px|||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 | ||
+ | |||
+ | [[Category:Plugins]] | ||
+ | [[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 |
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
[+]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