The Travel Distance Suite of Programs

Ryan Coleman, Sharp Lab, Fall 2009, version 3.0


These programs compute 2 useful depth metrics (Travel Depth and Burial Depth) and find 2 kinds of features of macromolecules (Holes and Pockets). The code is Python 2.5 based, uses FORTRAN for some operations, and integrates with utilities like PyMOL to display results. It is based on several lab publications by Coleman & Sharp:

Download the code and documentation (version 3.0.1 has fixes for numpy)





Travel Depth
travel depthtstTravelDepth.py




Burial Depth
tstBurialDepth.py

CHUNNEL finds tunnels
tstChunnel.py

CLIPPERS finds pockets
tstPocketMap.py
The Travel Distance code requires the installation of the following code:
  • Python 2.5 (2.6 may work)
  • Numeric (numpy also works but is slower for some reason)
  • PyMOL (for visualizing structures)
  • aiSee (for visualizing cluster graphs of pockets)
Funding Acknowledgements: Primary support from the NIH (GM48130) is gratefully acknowledged, as well as support from the NIH Structural Biology Training Grant (GM008275), the Computational Genomics Training Grant (T32HG000046) from the National Human Genome Research Institute, and the NSF (MCB02-35400).