BV_PeptideBuilder

Creating peptides from amino acid sequence

To manually build peptides one can use BALLView's Peptide Builder. Start it from the main menu

{{{ Build -> Build Peptide }}}

A dialog will show up, where you can either enter the aminoacid sequence in one letter code or use the amino acid buttons to define the sequence.

The Peptide Builder offers a group box Backbone to specify the torsinal angles for the given amino acids, e.g., helix, beta-sheet or arbitrary torsional angles.

Press the Build button in construct your peptide.

Note that a certain amount of amino acids must be selected to be able to build e.g. an helix.

BALLView can also visualize the secondary structure of a protein. If secondary structure was not given in the input file (e.g. pdb file) one should explicitly calculate the secondary structure via

{{{ Tools -> Calculate Secondary Structure }}}

The underling algorithm is the DSSP of Wolfgang Kabsch and Chris Sander.

For visualizing the secondary structure try our cartoon model colored by secondary structure. Use the right mouse button menu of your molecule in the Structures window and chose {{{ Create Representation -> Cartoon -> by secondary structure }}}