Workflow

TODO: describe the individual steps

Sample point generation

Path (1D)

  • str8path
  • HOLE

Volume (3D)

  • HOLLOW (custom version)

Parameter settings

Radii and Charges

Use pdb2pqr to generate the input PQR file.

BornProfiler run input file

  • …
  • membrane position
  • exclusion zone

Queuing system script

Discuss example, highlight what needs to be customized and how.

Generate window input files

::
apbs-bornprofile-mplaceion

Run jobs

Manually or typically through a queuing system.

Analyze and visualize data

::
apbs-bornprofile-analyze

Distinguish 1D/3D.

Talk about using Chimera to analyze 3D energy landscapes and add some tips & tricks.