Forster distance calculator

From PyMOLWiki
Revision as of 04:28, 24 August 2011 by Tlinnet (talk | contribs) (Created page with "== Author == This pymol script is made by Troels Emtekær Linnet<br /> == Introduction == This script can be handsome, if one is working with Förster resonance energy transfer ...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

Author

This pymol script is made by Troels Emtekær Linnet

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.