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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 be in this situation.

rama

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.