Calculate structure

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An important part of protein structure is the secondary structure which is made up of helices, sheets and turns, and Jmol has always been capable of determining and displaying these three types of structures with limitations as described in How Jmol Determines Secondary Structure . The calculate structure[1] is a command which has been more recently developed and does an objective identification of these secondary structures. Calculate structure by itself only identifies the different secondary structures and does not result in the display of a structure. Additional commands are required to color and render the secondary structures differentially and to display the hydrogen bonds (hbonds). The development of the scenes in this article included the use of the script select protein; calculate structure; cartoon; color structure. Since the post-green link processing of the calculate hbonds structure command is malfunctioning, it was not used when making the scenes. In order to display hbonds in any scene which does not show them, click on the Jmol frank, in the main menu click on Console, in the bottom box of the console enter the command calculate hbonds structure and then click Run. This same technique, with the exception of entering select protein; calculate structure; cartoon; color structure; calculate hbonds structure into the lower console box, can be used to do an objective identification of the secondary structures on any Proteopedia page in which it has not been done.

The objectives of this article are:

  • Describe briefly how calculate structure identifies secondary structures, with a focus on identification of β and γ-turns.
  • Summarize the observations obtained from using calculate structure to identify turns in two proteins.

Myohemoerythrin is shown in the applet below. ()


References

  1. A detailed description is at [1].
  2. 2.0 2.1 W. Kabsch & C. Sanders, Biopolymers, 22, 2577-2636, 1983.
  3. 3.0 3.1 Characteristics of β-turn classes
  4. Miner-White, EJ, et. al. One type of gamma turn, rather than the other, gives rise to chain reversal in proteins. J. Mol. Bio. 204, 1983, pp. 777-782.
  5. Open home page of PDB
  6. Open myohemerytherin at sequence page with Jmol open;   Open sequence and Secondary structure page
  7. Open glycogen phosphorylase, chain A (3np7.pdb) with Jmol applet displayed

Proteopedia Page Contributors and Editors (what is this?)

Karl Oberholser, Jaime Prilusky, Wayne Decatur

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