Rotkit

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Type Python Script
Download rotkit.py
Author(s) Troels E. Linnet
License BSD
This code has been put under version control in the project Pymol-script-repo

Introduction

This script-kit is a collection of small script to be able to precisely to put a molecule (like a dye) where you want in relation to a protein.

You can also create rotational states of a domain or simulate a dye freedom.

It simply makes the PyMOL TTT matrixes, in a easy and user friendly way. The calls to the functions available in PyMOL, takes care of all the conversion of input and such.

If you are interested in this, you might also want to check out the PyMOL Chempy module that is included in PyMOL. It provides handy vector and matrix functions.

Functions available in PyMOL

  • rotateline(Pos1,Pos2,degangle,molecule):
    "Pos1->Pos2" define a line whereabout "molecule" will be rotated "degangle" degrees
    rotateline Pos1=P513C_CA, Pos2=P513C_CB, degangle=5, molecule=Atto590
    rotateline Pos1=dyeatom87, Pos2=dyeatom85, degangle=10, molecule=Atto590
  • mutate(molecule,chain,resi,target="CYS",mutframe="1"):
    Mutate a /molecule//chain/resi into a target, and selecting most probable frame 1
    mutate 1HP1, chain=A, resi=515, target=CYS, mutframe=1
  • toline(Pos1,Pos2,atom,molecule,dist=1):
    Translate molecule atom, 1 angstrom away in the same direction Pos1->Pos2 specify
    toline Pos1=P513C_CA, Pos2=P513C_CB, atom=dyeatom87, molecule=Atto590, dist=3

Available through rotkit.functionname

  • printMat(matrix):
    prints the TTT matrix in a readable format. (4X4)
  • getxyz(Sel):
    output is a list [x,y,z] in float. The input can be a list, a string(list) or a selection.
  • vector(Sel1,Sel2):
    Finds the vector between points. Gets the xyz list from getxyz, so input can be anything.
  • vectorstr(vector):
    turn a vector in list format into string. No real function actually.
  • transmat(vector,dist=1):
    Makes a TTT translation matrix for according to the input vector. The vector is multiplied with dist.
  • unitvector(vector):
    Make a vector a unitvector.
  • radangle(angle):
    Convert degree to radians. Not that all input are assumed to be in degrees, and are converted automatically.
  • rotmat(angle,vectornorm,pointcoord):
    This function is the most important. That makes the TTT matrix that rotates a molecule around a normalized vector, which goes through a coordinate point.
  • crossprod(Vector1, Vector2):
    Makes a crossproduct between two vectors
  • crosspoint(Pos1, crossprod):
    Returns the endpoint for the Position plus the crossproduct vector. Suitable if one would like to rotate around a crossvector.

Example of use

Example 1 - Make a rotation of domain

Download: examples/rotkit_1.pml
This code has been put under version control in the project Pymol-script-repo

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Example 2 - Simulate dye freedom

Download: examples/rotkit_2.pml
This code has been put under version control in the project Pymol-script-repo

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Example 3 - Create distance distribution histogram

Download: examples/rotkit_3.pml
This code has been put under version control in the project Pymol-script-repo

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Example 4 - A tutorial file

To understand how the functions works, read through the tutorial. Hash/Unhash "##" each step at the time to see the effect. To be able to follow the tutorial, you need the dye molecule, which is loaded from the Pymol-script-repository.

Download: examples/rotkit_4.pml
This code has been put under version control in the project Pymol-script-repo

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