Transform odb

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"transform_odb" transforms the coordinates of a selection and creates a new object with the transformed coordinates. The transformation matrix is read from a specified "O"-style tranformation matrix file (.odb) written by "O" or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.


transform_odb name, (selection), matrix_file [, transpose]
  • name = object to contain transformed coordinates
  • selection = atoms to transform
  • matrix_file = file name or path of .odb file containing a transformation matrix data block
  • transpose (default 0]


transform moved_helix, ( mol1 and resi 200:220 ),  move_helix.odb




from pymol import cmd import pymol import os import re import string

def __init__(self): cmd.extend('transform_odb', transform_odb)

  1. Creates a new object name from selection after transforming it with O-style matrix
  2. found in matrix_file
  3. Author: Mark Saper <>

def transform_odb( name, selection, matrix_file='matrix.odb', transpose=0):

# open the file for reading matrix_file = os.path.expanduser(matrix_file) matrix_file = os.path.expandvars(matrix_file) theInFile = open ( matrix_file,"r")

# what we'll store the results in theMatrix = []

# read every line in the file and ... for theCurrLine in theInFile.readlines(): if (theCurrLine) and (theCurrLine[0] != '!') and (theCurrLine[0] != '.'): # if the line isn't blank, make a list of items seperated by tabs theNewRow = string.split (theCurrLine) # add it in the matrix theMatrix.extend ( theNewRow )

# change matrix to pymol unsupported format

theMatrix = [ theMatrix[0], theMatrix[3], theMatrix[6], theMatrix[9], theMatrix[1], theMatrix[4], theMatrix[7], theMatrix[10], theMatrix [2], theMatrix [5], theMatrix[8], theMatrix[11], 0.0, 0.0, 0.0, 0.0 ] theMatrix = [ float(x) for x in theMatrix]

# close the file theInFile.close ()

r = cmd.create ( name, selection) r = cmd.transform_object( name, theMatrix, transpose=transpose)

return r

cmd.extend('transform_odb', transform_odb)


transform_selection, transform_object