Generate ideal helices and strands

This script shows how to generate idealized helices and strands from a sequence.


For certain purposes, such as writing tests for cctbx, it is useful to generate a model of idealized secondary structure, such as helices and beta strands.


The script needs the following imports:

from __future__ import absolute_import, division, print_function
from import ss_idealization as ssb

The first line makes sure that the script runs with both Python2 and Python3.

The second import from the mmtbx/secondary_structure module makes available the function used to generate ideal secondary structure.

Then we create an ideal helix from a sequence, here we use the example sequence "ILMKARNDWYV":

ph_helix = ssb.secondary_structure_from_sequence(ssb.alpha_helix_str,"ILMKARNDWYV")

The secondary_structure_from_sequence function creates a new pdb_hierarchy object. The first argument is a string in PDB format (pdb_str) that has the geometry of the secondary structure. The following strings are available in the code; in parenthesis is the name of the variable in the code:

  • Alpha helix (alpha_helix_str)
  • 3-10 helix (a310_helix_str)
  • Pi-helix (pi_helix_str)
  • Beta strand (beta_pdb_str)

The second argument is the sequence, in form of a string of one-letter codes. It can be an explicit sequence, such as "ILMKARNDWYV", or in form of "A"*20 for 20 alanine residues.

Once we have the new pdb_hierarchy for the idealized helix, we can save it as PDB file:


Similarly, we can create an ideal beta strand:

ph_strand = ssb.secondary_structure_from_sequence(ssb.beta_pdb_str,"ILMKARNDWYV")


For the sequence used in our example ("ILMKARNDWYV"), we get the ideal alpha helix below.


For the same sequence, we get the follwing strand. Note the peptide N-H and C=O groups pointing to the top and the bottom.