interhlx is a C program that calculates the angle between two helices in a 
protein (PDB file) and the distance between midpoints of these helices.  
Each helix is represented by a straight-line vector, with the coordinates of
the vector endpoints defined as the average of the first (or last) ten atom
coordinate positions of each helix.

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This tar file contains:
- this README file
- an example input file and the corresponding PDB file for input
- an SGI executable (cc-compiled on an SGI O2 IRIX 6.3) "interhlx_sgi"
- a Sun (Solaris) executable (gcc-compiled on a SunOS5.5.1 Ultra 1)
  "interhlx_sun"
- a Linux executable "interhlx_lin"
- a MacOSX Panther executable "interhlx_mac" (gcc compiled on Darwin 7.0.0
  Thanks to Dr Jack Howarth, Univ of Cincinnati)

Please contact kyap@uhnres.utoronto.ca for source code if needed.

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Calling interhlx
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(The executable to be used can be renamed to 'interhlx', e.g.
 kyap% mv interhlx_sgi interhlx )


interhlx can be called in two ways:

kyap% interhlx file.pdb bgnhlx1 endhlx1 bgnhlx2 endhlx2 [chainID]
kyap% interhlx pdb_list output_file

The first invocation will print single angle/distance values to screen.
The second invocation will print lists of angles and distances as well as
averages and standard deviations to the file 'output_file'.  If this file
exists the user will be asked for permission to rewrite.


Input pdb_list format
---------------------

file.pdb bgnhlx1 endhlx1 bgnhlx2 endhlx2 [chainID]
pdbfile1 26 45 76 89
/home/jack/file2.pdb 26 45 76 89 B
/pdb_files/1pdb.ent 11A 34 39 42C

Each line of the file lists the filename (explicit in file location if 
interhlx is not called from the user's home directory), the start and end
points of the two helices, and an optional chain identifier (always one
character).  The chainID must be specified if there are two or more chains
in the pdb file.  Some files have this column (column 22) even though it may be
the only chain described; in these cases it is not necessary to indicate the
chainID.

As in the last line of the example filelist above, interhlx can now accommodate
residue numbers with a single-character icode.

interhlx also will take the helix assignments 76 89 26 45 to be equivalent
to 26 45 76 89.


Other notes
-----------

The maximum number of PDB files to be evaluated and averaged is 100.  However,
this is easily changed by editing the source code (available separately).

Sign convention is as described in Drohat et al. (1996) Biochemistry 
35:11577-11588.

The coordinates of the endpoints of the helix vectors are calculated by 
averaging the coordinates of the first (or last) ten backbone N, CA and C 
atoms.  Since there are 3.6 residues, or 10.8 backbone atoms per turn, the
first and eleventh atoms lie on a vertical line nearly parallel to the
axis of the helix vector.  Thus, using eleven atoms would result in average
coordinates weighted toward a particular region of the horizontal plane 
(perpendicular to the vector axis).

This program is downloadable from 

http://nmr.uhnres.utoronto.ca/kyoko/interhlx/