interhlx - Interhelical angle program (with sign designation) - Oct. 20, 1998

• program can now be called in one of two ways:
• diana% interhlx file.pdb bgnhlx1 endhlx1 bgnhlx2 endhlx2 [chainID]
• diana% interhlx pdb_list output_file

an example of a pdb_list file
the resulting output_file includes all angles and midpoint distances, with overall average and standard deviation.
an example of an output_file
• If output_file exists prior to program execution, the user will be given the choice to exit or rewrite the file.
• If one file in the output_file cannot be read, the program will skip it and move on (instead of terminating).
• The helix endpoint assignments "76 89 26 45" are taken to mean "26 45 76 89".

Read the README file

Thanks to Dr Jack Howarth (U of Cincinnati) for the Darwin executable.

There is no published paper associated with the program, although something like the following would be adequate:

"..interhelical angles were calculated using interhlx (K. Yap, University of Toronto).."

The interhelical angle reported by interhlx is 180 degrees minus angle theta reported by the program VGM.  If this is noted (and since the latest version of interhlx uses code from VGM), then the following may be cited:

Yap, K.L., Ames, J.B., Swindells, M.B. & Ikura, M. (2002) Vector Geometry Mapping: a method to characterize the conformation of helix-loop-helix calcium binding proteins.  Methods Mol Biol 173:317-324.  [Medline] [PDF]

• option to output lists of angles/distances plus averages and SD to screen.
• accommodation of lines longer than 80 characters in the pdb_list file.
• allowance of different chainID for each helix.