Documentation for the HOLE suite of programsDocumentation for the HOLE suite of programsCopyright 1997 by Oliver S. Smart
Visualization of the cavity running through the channel structure of gramicidin A determined by Arseniev and co-workers. The HOLE representation of the internal surface of the pore is shown in a multicoloured form produced by sphqpt program. Red marks places where the pore radius is below 0.6 Å, green is used where it is in the range 0.6Å to 1.15Å and blue marks places where it is above 1.15Å. AMBER values where used for van der Waals atomic radii (file simple.rad is used). A radius of 1.15Å is the minimum required for a water molecule showing that this form of gramicidin would be filled with solvent molecules under normal conditions.
If you are not using a modern version of netscape then may I recommend you obtain one - its free to non-profit people. If you do not have access to a web browser then as a last resort postscript versions of the documentation are available by anonymous ftp.
email: osmart@pugh.bip.bham.ac.uk
www:
O.S. Smart
(http://www.cryst.bbk.ac.uk/~ubcg8ab/smart.html)
snail mail:
phone: +44 (0) 121 414 4090 (Direct)
fax: +44 (0) 121 414 3982
1.0 Distribution conditions1.1 Formal Notice
1.2 Acknowledgements
2.0 Introduction & Setup 2.1 Brief Scientific background:
2.2 Copy of J. Mol. Graphics article giving
overview of HOLE
2.3 New features for release 2
2.4 Acquiring the package
2.5 Setting up the package
3.0 Control of HOLE 3.1 Cards which must be specified:
COORD,
RADIUS,
CVECT ,
CPOINT
3.2 Cards which may be specified:
4.0 Tips on using HOLE, Sample input file 5.0 van der Waals radii files 6.0 Visualization of HOLE results
6.1 Plotting 2D Graphs
6.2 Using molecular graphics:
6.3 Colours used in HOLE
6.4 Getting hard copy pictures
6.5 Creating 2D Maps of the internal surface of a pore
7.0 Ancillary programs
7.1 qpt_conv convert HOLE .qpt file for use with another program (e.g., sybyl)
7.2 sphqpt (produce HOLE .qpt from a ".sph" file)
7.3 qplot (produce postscript picture of .qpt files)
7.4 labqpt (produce .qpt file with labels
for particular atoms)
7.5 vdwdot (calculate internal van der Waals surface)
7.6 sph2vrml (produce pretty vrml file from a sph file)
7.7 make_post_map, bln2gnu, capost2gnu, grd2gnu,
make_post2gnu
8.0 Using HOLE to predict conductance properties of
ion channels
8.1 Absolute conductance predictions in KCl
8.2 Predicting the effect of adding non-electrolytes to
conductance experiments
9.0 An example run: analyzing the cavity in
the Arseniev gramicidin structure 10.0 Future Developments and Applications to date
10.1 Potential Developments
10.2 Applications to date
If anyone else has access to the code/executables mounted in your space then it is your responsibility to ensure that they abide by these conditions.
You must reference any use made of HOLE in published work by citing:
