We give here a description of the MolAxis input parameters and results window. We also explain how to use the stand-alone version of MolAxis. See the tutorial tab for a step by step example of how to use the stand-alone version.
The input fields of MolAxis are:
In chamber mode with multiple channels (which is the default), the results page contains a table that describes all of the detected channel. Each row in the table contains the bottleneck radius, bottleneck residues, and split radius of the channel. Click the channel checkbox and residue name to display in the Jmol panel on the right.
In TM mode and in chamber mode with a via sphere, the results page contains a detailed table that reports the radius and residues along the discovered channel.
The button 'Hide residues' removed from the jmol window all residues. The checkbox 'Toggle all spines' shows/hides the spine of all of the channels.
The 'Windows' and 'Linux' links contain full text files (in Linux and Windows format) of the run. For each channel there are files that describe the channel radius, lining residues and bottleneck properties.
Additional control over representation of the molecule can be obtained
using Jmol control panel by right clicking on the viewer window. In
this panel, representation of the molecule
(ribbons/cartoons/sphere/wireframe etc.), colors and more can be
changed. For more advanced commands the Jmol console window can be
opened from the panel. For more information on Jmol see Jmol website.
A list of advanced parameters:
Open the tar file 'download.tar.gz' in a new directory, such as ~/molaxis. Set the enviroment variable $MOLAXIS_ROOT to this directory, for example:
% set MOLAXIS_ROOT=~/molaxis
Add this variable to your .basrc (or .cshrc) file.
After the installation edit and update the atom radii in the radii file $MOLAXIS_ROOT/ini/radii.txt. MolAxis comes with default radii values.
Usage: molaxis [command] -pdb [filename] [optional paramaters]
See the README file for a detailed description of the molaxis syntax.