Biopolymer

1       Introduction

The commands in the Biopolymer module facilitate the building and modification of peptides, proteins, polysaccharides and nucleic acids. In particular these commands can be used to:

Capabilities of Biopolymer

• Build up peptide sequences while imposing secondary structure; delete and replace residues. (Protein and Residue pulldowns).

• Build and modify molecular models of nucleic acid compounds. (Nucleic_Acid and Nucleotide pulldowns).

• Construct polysaccharides, alter or change an existing monosaccharide in a polysaccharide and join polysaccharides together (Carbo pulldown).

• Predict the backbone conformation of a protein from its -carbon trace. (Backbone command).

• Search for the optimal division of the protein structure into a set of separated domains. (Domain_Analysis command).

• Query a protein database and retrieve matching fragments (Str_DB pulldown).

Invoking Biopolymer

Pilot tutorials

To start Pilot, click the mortarboard icon on the Insight II toolbar. When the Pilot interface appears, click Select and choose the Biopolymer tutorials from the list.

Select any of the listed tutorials and click the Select button. Run the tutorial by clicking either of the two leftmost buttons at the top of the Pilot window.

These two buttons will execute a single command from the tutorial. The leftmost button executes commands without displaying the graphical user interface, while the adjacent button displays the interface containing predefined command parameters and waits for the user to click the execute button in the user interface parameter block.