Forster distance calculator

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

Contents

Introduction

This script can be handsome, if one is working with Förster resonance energy transfer in proteins. The script calculates the Förster distance: R0, from two dyes excitation/emission spectres.
This script is very handsome, if one want's to pick two dyes from different companies, and the Förster distance is not provided in a table.

This script does no calculation of proteins in pymol, but is made as a "hack/shortcut" for a python script.
We use the python part of pymol to do the calculations, so a student would not need to install python at home, but simply pymol.

Spectre input

There should be provided the path to four datafiles:
Excitation and Emission spectre for the Donor dye: D_Exi="path.txt" D_Emi="path.txt
Excitation and Emission spectre for the Acceptor dye: A_Exi="path.txt" A_Emi="path.txt

Each of the files shall be a two column file. Separated by space. Numbers are "." dot noted and not by "," comma. One can for example prepare the files by search-and-replace in a small text editor.
The first column is the wavelength in nanometers "nm" or centimetres "cm". Second column is the arbitrary units of excitation/emission. For example:

Absorption
Wavelength "Alexa Fluor 488 H2O (AB)" 
 
300.00 0.1949100000 
301.00 0.1991200000 
302.00 0.2045100000 
303.00 0.2078800000 
....

Getting spectres

For example provides the company ATTO-TEC spectre for their dyes in excel format Spectre(excel-file). These can easily be copied from excel to a flat two column file.

Some of the most cited dyes are the Alexa Fluor dyes from the company invitrogen. Invitrogen does not provide spectres for their dyes in dataformat, but as flat picture files.

Luckily, a group on University of Arizona have traced several spectre of dyes from the literature with a graphics program. They have made these spectre easily public at http://www.spectra.arizona.edu/. I highly recommend this homepage. With these Spectra, the script can calculate the Forster Distance for different dyes from different companies.

Download one spectrum at the time by "deselecting" in the right side of the graph window. Then get the datafile with the button in the lower right corner.

Input values

The calculation needs input for:

How the script works

The output is a text file, with all the datapoints.

  1. Column: Donor: The input Emission wavelength.
  2. Column: Donor: The input Emission, arbitrary units of excitation.
  3. Column: Donor: The input Emission, arbitrary units of excitation, divided by the integrated area.
  4. Column: Acceptor: The input excitation wavelength.
  5. Column: Acceptor: The input excitation e(molar extinction coefficient).
  6. Column: Acceptor: The input excitation e(molar extinction coefficient), scaled correctly.
  7. Column: The calculated overlap for this datapoint.
  8. Column: The summed values for calculated overlap, until this datapoint.


It also automatically generates a gnuplot .plt file, for super fast making graphs of the spectres. In linux, gnuplot is normally part of the installation. Just write: gnuplot FILENAME.plt If you are in windows, download gnuplot and open the .plt file.

Gnuplot makes three graphs in .eps format. They can be converted to pdf with the program: epstopdf or eps2pdf. They are for example part of LaTeX: C:\Program Files (x86)\MiKTeX 2.9\miktex\bin or you can download it here. The format of .eps is choses, since gnuplot then allows for math symbols in the graphs.

How to run the script

Make a pymol .pml file like this. Write in the required information, and execute/run the script with pymol. Then open the .plt file afterwards with gnuplot.

## Change to your directory
cd /homes/YOU/Documents/Atto-dyes/Spectre/ALEXA488-ALEXA633
import forster_distance_calculator
forster D_Exi=ALEXA488Exi.txt, D_Emi=ALEXA488Emi.txt, A_Exi=ALEXA633Exi.txt, A_Emi=ALEXA633Emi.txt, A_e_Max_Y=159000, A_e_Max_X=621, Qd=0.92
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