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Written by: Melanie Nelson, 10/15/98
The program interhlx (written by Kyoko Yap in Mitsu Ikura's lab at the University of Toronto) will calculate the angle between two helices, including the sign, in a structure or a family of structures. If the program is run on a family of structures, the output includes the angle for each member of the family as well as the average angle and standard deviation.
How the program calculates the sign of the angle:
The program uses the following convention to calculate the sign
of the angle between two helices:
The two helices are taken to be positioned such that helix I
is "in front of" helix II.
Helix I (from N to C) is used to define a vertical vector. A second
vertical vector is defined, with its tail at the C-terminus of
helix II. The angle between helices I and II is the rotation required
to align the head of the second vector with the N-terminus of helix
II. The vector is rotated in the direction (clockwise or
counterclockwise) that produces an angle of less than 180 degrees.
If the rotation is clockwise, the sign is positive. If it is
counterclockwise, the sign is negative.
It seems that the program can only run if helix I comes before helix II in the protein's sequence. The program will hang if the order is reversed.
Obtaining the program: People at TSRI can find the SGI executable in /usr/local/bin on bianca. People from other institutions will need to contact Kyoko Yap directly to request a version of the program.
Using the program: The program reads the pdb files and the
limits of the helices from an input file. The format of the input
file is:
pdbfile hlx1_start hlx1_end hlx2_start hlx2_end
The program can handle families of structures. Each structure in the
family should be in a separate file, and each file should be listed
in the input file:
pdbfile1 hlx1_start hlx1_end hlx2_start hlx2_end
pdbfile2 hlx1_start hlx1_end hlx2_start hlx2_end
pdbfile3 hlx1_start hlx1_end hlx2_start hlx2_end
etc.
Here is a handy trick to generate a list of the pdb files in an
input file, stolen from UNIX Power Tools by Jerry Peek, Tim
O'Reilly, and Mike Loukides:
Open a new vi session:
vi
Issue the following command in the vi session to read in a list of
files ending with the pdb extension:
:r !ls *.pdb
Write the list to a new file:
:w filename
If you want to calculate more than one interhelical angle you can either: 1) run the program repeatedly, once for each interhelical angle, altering the input file between each run, or 2) make one big input file listing all the pdbfiles for each set of helical limits, as shown in this sample input file provided by Kyoko Yap.
To run the program, type:
interhlx inputfile outputfile
The output file must be empty. If you are not running in the
directory in which the pdb files are stored, you will have to
include the complete path to these files in the filenames in the
input file:
/home/userX/directoryX/pdbfile1 hlx1_start hlx1_end hlx2_start hlx2_end
However, there seems to be a limit to the length of the pathname that
the program can accomodate. If the pathname is too long, the program
will return an empty output file.
If you get output that looks something like this:
Angle nan0x7ffffe00 Distance nan0x7ffffe00 ____________________________________________________________ Average Std dev Std dev Angle nan0x7ffffe00 +/- nan0x10000000 Distance 0.000 +/- 0.000 ____________________________________________________________