interhlx - Interhelical angle program (with sign designation) - Oct. 20,
Sign convention is as described in Drohat et al. (1996) Biochemistry
program can now be called in one of two ways:
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
Download SGI/Solaris/Linux/MacOSX Darwin executables,
sample input/output files and README file
(untar into directory called 'interhlx': tar xvf interhlx.tar)
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
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]
Thanks to W. Chazin, M. Nelson and L. Mäler for suggestions for improvement.
option to output lists of angles/distances plus averages and SD to screen.
accommodation of lines longer than 80 characters in the pdb_list
allowance of different chainID for each helix.