Software

SFG_AmideI_GUI

version 0.9.6 Download

SFG_AmideI is a SFG/2DSFG simulation package base on Matlab script language. This package focus on SFG/2DSFG spectrum simulation of coupled Amide I vibrational modes. Given a PDB file, the code can simulate its FTIR/1DSFG/2DSFG spectrums. This code also come with the ability to draw the transition dipole direction and molecule in ball and stick model.

To run SFG_AmideI, please download the package and extract into your MATLAB default folder. In the extracted folder you can exectue "SFG_AmideI.m" and you should see a GUI interface pop-up. 

To start with, you can select example PDB files by click "Load PDB file" buttom. There are two example PDB file: 20-glycine-helix-z.pdb and 2RRI.pdb. The 20-glycine-helix-z.pdb is an ideal alpha helix and 2RRI is a real helix download from Protein Data Bank. You can also load in your own molecules. The suggest path for input pdb file is the "PDB_Files" folder under the main package path.  

As an example, we start with "20-glycine-helix-z.pdb". After loading "20-glycine-helix-z.pdb", the script will generate a simulated SFG spectrum with default input variables. You can also chage the default input by edit the Input box on GUI. Once the default values has been chaged, you can update the figure by click corresponding buttoms.

This package can also simulate a isotope labeled spectrum. For example, if I have the first 3 residure and the 5th residue being labeled by 13C=18O, I can type "1:3,5" in the "Index of labeled residue" box and update with a proper vibrational frequency (here I choose 1590 for demostration) in "Labeled Frequency". 

For 2DSFG simulation, you can click the "Plot 2DSFG" buttom. Depends on the size of molecule, it take from few seconds to few minutes to generate a spectrum. For example, using the ideal helix with isotope labele on the fisrt to the third and the 5th residue, one should see this spectrum in about few seconds.

For more information please find the README.txt file in the package. If you have any question yo can also contact me through email