Difference between revisions of "Bnitools"
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== Menu functions ==
== Menu functions ==
# BNI tools dropdown menu
# BNI tools dropdown menu
Revision as of 04:58, 20 April 2016
|This code has been put under version control in the project Pymol-script-repo|
The bnitools is a plug in for PyMOL which adds additional functionalities and presets to the PyMOL GUI.
Linux and Windows
This plugin is distributed through the project Pymol-script-repo
Install it using the 'Install Plugin' menu within PyMOL:
PyMOL > Plugin > Plugin Manager
# 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