cd tar xzf hole2.2_002_linux.tar.gzThese commands will create the directories:
~/hole2/exe/hole *** Program HOLE *** If results of this run are reported or published, please cite the publications listed below. (edited for brevity) Control variables read:The hole program should start and wait for input - hit ctrl-d (the control and d keys together) to get out of this or ctrl-c to interupt. If the program fails to load then please goto the hole homepage help section: http://hole.biop.ox.ac.uk/hole/help
- If you are a tcsh or csh user add the following line at the end of your ~/.cshrc filesetenv PATH "$PATH":~mary/hole2/exe
- or otherwise if you are a bash user add the line that follows to the file that is used to set your ENV. This file is normally called following ~/.bash.profile or ~/.profile or ~/.kshrcPATH=$PATH:~mary/hole2/exe(if unsure which shell you are running type echo $SHELL)
The user must supply a file containing the co-ordinates for the ion channel structure to be analyzed - in pdb format. Atom records are read and the van der Waals radius of each atom is set up. In the original version the user had to supply an initial point in the channel cavity and a vector in the rough direction of the channel, now HOLE has the facility to make guesses for these. HOLE then proceeds to move the point on the plane normal to the channel vector so as to find the largest sphere which can be accommodated without overlap with the van der Waals surface of any atom. The optimization is achieved by a Monte Carlo simulated annealing procedure. This method was initially chosen to avoid becoming trapped in local "minima" but has subsequently proved to be useful in follow alternative routes through channels with a complex internal cavity, such as annexin V (Smart, Wallace and Goodfellow, 1993). Once the largest sphere which can be accommodated on a particular plane is found a small displacement is taken in the direction of the channel vector and the process is repeated for the next plane. The net result of the routines is a series of sphere positions that can be thought of a flexible sphere "squeezing" through the ion channel.
Output from the procedure is in three forms:
As well as being able to read from multiple pdb files HOLE can now read from CHARMm .DCD format binary trajectory files. Details of this option can be found by looking at the CHARMD and CHARMS cards.