Analysing an active site


Building Loops


Building a functionnal unit from a monomer


Crystal Symmetries


Electron Density Maps


Energy minimisation


Fitting Residues into Electron Density


Homology modelling


Making Phi/Psi statistics


Superposing Proteins






Last modified
31 March 98
by N.Guex


Tutorial : Making Phi/Psi Statistics

In this example, we will display a Ramachandran plot, learn how to detect CIS amino-acids, and collect some backbone torsion angles.

Step by Step

  • First of all, open the pdb file 1ldm (this file is included in the tutorial package).


  • Choose the "non-trans" item of the "Select" menu and click OK.


  • Choose the "Show Ramachandran Plot" item of the "Display" menu.


  • Choose the "Colour by Type" item of the "Display" menu.

At this stage, you should see something like this.

Now, you can move the dot over any point to know which residue it is.


  • Now, select the "Save" item of the "File" menu. This will write a tab-tabulated text file containing the omega/phi/psi angles of the currently selected amino-acids (see below).
          entry     secondary 
           name  aa   struct    omega    phi      psi  
           1ldm  THR         -174.042 -113.455  150.350
           1ldm  GLU         -173.445  -67.249  143.847
           1ldm  LYS         -173.490  -95.261  137.654
           1ldm  ILE   H      174.125  -43.002  -49.334
           1ldm  ASP          174.025  -93.739   -2.536
           1ldm  PHE         -171.111  -98.524   27.250
           1ldm  LEU         -174.899 -148.073 -174.787
           1ldm  ALA         -170.314  -68.300  -23.500
           1ldm  LYS   S     -173.173 -142.321  123.422
           1ldm  TYR   H     -173.366  -63.933   11.001
           1ldm  SER          174.528  -75.204  144.844

Obviously, there are too many non-trans residues. By having selected the default value of 175° in the dialog, you have selected all slightly distorted residues.

  • So, choose the "non-trans" item of the "Select" menu type 90 and click OK. This will select only residues with an omega torsion angle inferior to 90° (In the case of 1ldm, only Pro139).


  • Hit the "return" key, and then the "=" key of the keypad (right mouse button for PC users). Now select the "torsion tool" of the main display window and click on any atom. You will have a numerical feedback of omega, phi psi angles for this residue.


  • If your "Caps-lock" key is down, hit "esc" to exit from this repeated torsion angles measurement mode.


  • An other interesting option is the one allowing to automatically select residues with bad backbone conformations. You can do so with the "Select AA with Phi/Psi out of Allowed regions" item of the "Select" menu. In the case of 1ldm, only three residues other than Gly have unusual backbone angles (Asp220, Asp276, Gln222) the two first being very close to allowed regions.