| 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 09 Feb. 2000 by N.Guex & T.Schwede |  | # 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. ``