Documentation for the HOLE suite of programs

Birmingham University and Birkbeck College CrestsDocumentation for the HOLE suite of programs

Oliver S. Smart and Guy Coates
School of Biochemistry
University of Birmingham


Originally developed at:
Department of Crystallography, Birkbeck College, University of London

Copyright 1997 by Oliver S. Smart



pretty picture of HOLE cavity through the channel form of gramicidin

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.


Note: this document is supplied as a file "~/hole2/doc/hole_d00.html" with each released version of HOLE - if you have the program then you should be available to view it locally by typing hole_help at the unix command line.

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.


Contacts

* email: osmart@pugh.bip.bham.ac.uk  comments?
* www: O.S. Smart (http://www.cryst.bbk.ac.uk/~ubcg8ab/smart.html)
* snail mail:
Dr Oliver S. Smart
School of Biochemistry
The University of Birmingham
Edgbaston
Birmingham B15 2TT
England
* phone: +44 (0) 121 414 4090 (Direct)
* fax: +44 (0) 121 414 3982
For release 2 beta.002 - May 1997, modified for move to Birmingham October 1997.


Contents

* 1.0 Distribution conditions

*1.1 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:
The most useful cards: PLTOUT, DOTDEN, SAMPLE, SPHPDB, ENDRAD, CAPSULE, IGNORE, 2DMAPS, CHARMD/CHARMS.
Other cards: DOTOFF, SPIKES, LINON, CENOFF. MCDISP. MCKT. MCSTEP. RASEED, SHORTO, MOLQPT, STOP.

* 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:
with: quanta, sybyl, O, mage, insightII, rasmol, VRML
* 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
......(programs used in making 2D surface map of the inside of a channel)

* 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


1.0 Distribution conditions for the HOLE suite of programs

HOLE and ancillary programs are supplied with source code free to non-profit making organizations. This is on the understanding that they will not be passed on to any third party. If any one wants to use the program get them to contact me - this will help me keep a list of users to be informed about developments, bugs etc.. Also details of any modification/improvement made must be sent to me - so that everyone else can benefit (all rights to modified versions of any of the programs will remain with the author and Birkbeck College). It should be noted that the code and notes are at an early stage of development and therefore the responsibility for their use and correctness of results lies with the user rather than me or Birkbeck College. You may incorporate any of the routines supplied in software of your own provided: (a) I am notified and (b) the complete software is supplied free to any non-profit making organization.

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:

O.S. Smart, J.M. Goodfellow and B.A. Wallace (1993)
The Pore Dimensions of Gramicidin A
Biophysical Journal 65:2455-2460.
.
And any relevant subsequent publications.

1.1 Formal notice

This documentation and software is an unpublished work containing confidential and proprietary information of Birkbeck College. Use, disclosure, reproduction and transfer of this work without the express written consent of Birkbeck College are prohibited. This notice must be attached to all copies or extracts of the software.


1.2 Acknowledgements

Original Release
The support of the UK Science and Engineering Research Council under project grant GR/G49494 and from the Molecular Recognition and Computational Science Initiatives is gratefully acknowledged. I should like to thank Julia Goodfellow and Bonnie Wallace for support and many discussions. Thanks are also due to Mark Sansom and his group at the University of Oxford, and Karen Duca of Brandeis University for testing the first release. In addition thanks to Rod Hubbard and Polygen/Molecular Simulations Inc. for providing the 3D plot file facility in HYDRA and QUANTA. QUANTA is available from Molecular Simulations Inc., Waltham, MA 02154, USA. InsightII is available from Biosym Technologies, 9685 Scranton Road, San Diego, CA 92121 - 2777 USA.

release v2.
The generous support of the Wellcome Trust by the provision of a Career Development Fellowship for the author is gratefully acknowledged. Much of the work undertaken was encouraged by Dr Mark Sansom and members of his group at the University of Oxford. Thanks to Valeriu Niculae and Joe Neduvelil for contributing to the programming as students at Birkbeck.


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Copyright 1997 by Oliver S. Smart

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