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.

• Channel Type: Select between 'Chamber' and 'Transmembrane' channels.
• PDB: It is possible to specify the PDB code of the input molecule or upload file in PDB format.
  Each code is a four character PDB ID, followed by a colon and a list of chain IDs, e.g. 2pka:AB. If no chain IDs are given,
  all the chains of the PDB file are used.
• e-mail address: The link with the results of your request is sent to this address. Using this link you can view MolAxis results. This field is optional.
• Source type: Is the starting point for channels search.
  can be either the largest void in the protein that will be detected automatically or a user defined starting point.
  
• User source sphere: Coordinates of the user defined source point.
• Channel vector: The approximate direction of the TM channel. This field is needed only for Transmembrane channels.

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.

Advanced Input Fields

A list of advanced parameters:

• Resolution: The resolution of the channel search (default 0.5A)
• Split distance: Above this distance pathways spliting are igoned (default 4A).
• Bounding sphere radius: Maximal channel length (default 30A).
• End channel at radius: Do not show channel radiuses abobe this value (default 4A).
• Include hetatoms: By default all hetatoms are ignored. Use this field to force MolAxis to take into account a list of one or more hetatom. For example, in order to include ZN and CU type "ZN CU".
• Include hydrogens: By default hydrogens are discarded. Use this field to take into account hydrogens.
• Mesh quality: The mesh quality controls the quality of the mesh generated for the jmol view.
• Via sphere: If used, MolAxis will report the optimal channel that passes through the given sphere.
• Radii table: MolAxis uses a default radii table. To use a set of user-defined atom radii values upload a file in the format of the example files.
• Probe radius: The radius of the probe sphere (default is 1.4).