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 = new or modified object that will contain transformed coordinates
  • selection = selection of atoms to transform
  • matrix_file = file name or path of .odb file containing a transformation matrix data block
  • transpose (default 0]


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


Please send questions or bug reports to Mark Saper,


from pymol import cmd
import pymol
import os
import re

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

# Creates a new object name from selection after transforming it with O-style matrix
# found in matrix_file
# 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 = theCurrLine.split ()
		  # 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