Dynamic secondary structure figures

In barnaba it is possible to create secondary structure figures showing the variability in the annotation within a set of structures. As an example, we generate this figure using all hits from the example example_06_single_strand_motif. Note that this functionality is only available as a command-line tool.



In [17]:

    
import os

# annotate structures
cmd = "barnaba ANNOTATE --pdb gnra_loops_*.pdb -o dynamic_ss"
os.system(cmd)
# this produces two files containing the annotations


# call SEC_STRUCTURE and specify stacking/pairing annotation files
cmd = "barnaba SEC_STRUCTURE --ann dynamic_ss.ANNOTATE.stacking.out dynamic_ss.ANNOTATE.pairing.out -o dynamic_ss"
os.system(cmd)
%ls dynamic_ss*.svg









    



dynamic_ss.SEC_STRUCTURE_167steps.svg

We now look at the .svg figure



In [ ]: