FAQ Notebooks

• Missing Contacts
  • ctc_cutoff_Ang
  • ctc_control
    • Controlling with integers
    • Controlling with fractions
  • n_nearest
  • Interfaces: ctc_control and min_freq
  • Interfaces: self_interface
  • Interfaces: AA_selection
  • Finally
• Controlling Flareplots
  • The scheme option in plot_freqs_as_flareplot
    • scheme=='all'
    • Unused Space : scheme='interface'
    • Unused Space: scheme=interface_sparse
  • Using the Blank Space
    • Consensus Labels
    • Unused Sub-fragments: scheme='consensus_sparse'
    • Unused Residues: scheme='residues'
  • Coarse-Graning Flareplots: Chord Diagrams
• Comparing Contact Frequencies: Bar Plots
  • The Data
  • Step-by-Step Refining of the Comparison-Plot
    • Figure Size
      • Using figsize
      • Using inch_per_contacts=1 (or some other numeric value) together with figsize=None
    • Removing Identities
    • Removing Small Values
    • Visual Aides
    • Consolidating the Plot
    • Showing Fragment Information: Informative Labels
    • Using Fragment Information: Sorting by Interface Side
  • Sorting by Standard Deviation
  • Coloring
• Comparing Contact Frequencies: Flareplots
  • The Data
  • One Single Flareplot
    • Including Fragment Information
    • Including Secondary Structure Information
    • Highlighting Residues
    • Tweaking the flareplot after plotting: flareplot attributes
  • Multi-Panel Figure
    • Common Background: Comparing Panels
  • Overlaying Flareplots
  • The Lower-Level Method freqs2flare
  • Plotting Frequency Differences