If you’re a Windows user I can suggest installing Oracle VirtualBox and in it an image of ubuntu 11.10.

Follow the instructions but beware of installing ubuntu 12.10 - In at least two desktops this operated extremely slow and practically unusable via VirtualBox.

For more tips on using Aviz you may vist Riki Hihinashvili's website, and be sure to check out the official Aviz website.

IRPS.tar.gz containg a view.vpm file and the executable test.exe

unzip with the following command:

tar -xf IRPS.tar.gz

sudo apt-get install monodevelop

With Mono you may view and edit my source code project test.tar.gz, and ofcourse - Mono makes it possible for you to create your own c# program and GUI in Linux, get acquainted with a hello world! tutorial.

Choose Nc: The total number of base-pairs (sites) of the chain.

I recommend starting at the order of 100 first, then work your way up until you gain the proper control over the settings.

This property is very relevant for the search. As the chain grows in length the longer it takes for the searching protein to find its target.

Choose dX: In um, this represents the distance between consecutive centers of base-pairs.

I recommend dX should in the order of 1 first.

This property is very relevant for the search. When choosing your diffusion constant and dT later on these properties must comply: 2*D*dT/dX^2 < 1

Choose dS: In um, this represents the distance between the DNA strands (distance between two molecules in each base-pair).

In order to view bonds in aviz please set dS lower than 10.

* This property is not relevant for the search model, it’s here to help you construct a chain of your liking.

Choose theta: In mrad, this represents the bend angle off the current DNA axis for the next step.

Please set lower than 300.

* This property is not relevant for the search model, it’s here to help you construct a chain of your liking.

Choose phi: In mrad, this represents the azimuthal turn angle for the next step.

Please set lower than 500.

* This property is not relevant for the search model, it’s here to help you construct a chain of your liking.

Choose seed: Select a large odd number that would be used as the seed for the c# Random Generator.

Choose Nrand: Select a number (preferably larger in magnitude than Nc) to be the size of the random numbers vector.

The simulation uses the random numbers vector in different types of iterations at the different phases, once the vector is totally used it is recycled.

Choose target: Select the index of the target site: between 0 and Nc-1.

The search process is complete when the protein is located at the target site (first passage).

Choose Xi: Select the starting point index of the target: between 0 and Nc-1.

Note that selecting Xi=target is cheating!

Choose D: In um^2/ms, the 1 dimensional Diffusion constant.

Remember that D, dX and dT must comply: 2*D*dT/dX^2 < 1.

Choose tau1: In ms, the typical time scale (of an exponential distribution) for a protein DNA slide.

Choose tau2: In ms, he typical time scale (of an exponential distribution) for a protein 3d excursion.

Choose dT: In ms, the time step of each discrete iteration. This is the most critical search property!

Remember that D, dX and dT must comply: 2*D*dT/dX^2 < 1.

Also, dT must be smaller than the time scales tau1 and tau2.

In general, a smaller dT gives the best approximation to the theoretical 1 dimensional Diffusion. The problem by setting dT too low is the sharp increase of iterations and frames needed to see progress in a search.