Mole 2.5 Command Line Output Help

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Output Types

Mole 2.5 Command Line generates these types of output:

  • XML for Channels (Tunnels, Pores, Paths), Cavities, Charges, and Start Points.
  • PDB for Channel profiles and lining residues.
  • CSV for Channel profiles and "centerline charges".
  • PyMol for Channels, Cavities, and Charges (surface and centerline potential).
  • Mesh for Channel surfaces, Cavities (can be loaded by JMol), and Start Points.

Note on Pores: There are 3 types of pores - Auto (computed automatically from openings inside the proteins), Merged (created from merging two tunnels) and User (created from custom specified end points).

Output Structure

All output data are located within the WorkingFolder directory.

  • XML is stored in the xml folder, and in ChargeName/xml for charges.
  • PDB is stored in the pdb folder, no extra PDB output is available for charges.
  • CSV is stored in the csv folder, and in ChargeName/csv for charges.
  • PyMol is stored in the pymol folder, and in ChargeName/pymol for charges.
  • Mesh is stored in the mesh folder, no extra PDB output is available for charges.

Note on Pores: Pores are exported in two categories - "Merged Pores" and "Pores" (this category contains Auto and User pores together).

Output Specs Overview

The format of the output data is in most cases self-explanatory. This section provides a description of its general shape.


Residue Format

Residues are exported in the format NAME NUMBER [CHAIN] [i:INSERTIONCODE] [Backbone] (arguments in [] are optional).

In some cases, chain is not specified (= empty record in PDB file).
Backbone indicates that the residue is orientated towards the channel with its main-chain.
Examples: HEM 508 A, ALA 103 i:A, HIS 203 B Backbone.


General shape of the XML:

<Tunnels Version="" FoundOrigin="1" Timing="1440">
  <Tunnel Id="1" Cavity="1" Auto="0">
    <Properties Charge="1" NumPositives="2" NumNegatives="1" Hydrophobicity="-0.67" Hydropathy="-1.99" Polarity="25.03" Mutability="81" />
      <Node Radius="1.556" FreeRadius="1.556" T="0.00000" Distance="0.000" X="-25.007" Y="-25.093" Z="-14.627" />
      <Node Radius="1.603" FreeRadius="1.603" T="0.01429" Distance="0.078" X="-24.999" Y="-25.066" Z="-14.700" />
      <Node Radius="2.541" FreeRadius="3.543" T="1.00000" Distance="8.815" X="-29.583" Y="-29.076" Z="-16.942" />
      <!-- The last node also determines the length of the tunnel -->
      <ResidueFlow>ARG 212 A,GLU 308 A,SER 312 A,LEU 482 A,GLN 484 A,LYS 173 A</ResidueFlow>
      <HetResidues>HEM 508 A</HetResidues>
      <LayerWeightedProperties Hydrophobicity="-0.87" Hydropathy="-2.37" Polarity="23.56" Mutability="88" />
      <Layer MinRadius="1.55623" MinFreeRadius="1.55623" StartDistance="0.00000" EndDistance="0.63649" LocalMinimum="0">
        <Residues>ARG 212 A,GLU 308 A</Residues>
        <Properties Charge="0" NumPositives="1" NumNegatives="1" Hydrophobicity="-0.78" Hydropathy="-4.00" Polarity="50.95" Mutability="80" />
      <Layer MinRadius="1.93902" MinFreeRadius="2.00252" StartDistance="0.63649" EndDistance="2.09516" LocalMinimum="0">
        <Residues>ARG 212 A,GLU 308 A,SER 312 A</Residues>
        <Properties Charge="0" NumPositives="1" NumNegatives="1" Hydrophobicity="-0.84" Hydropathy="-2.93" Polarity="34.52" Mutability="92" />

In the case of pores and paths, the root element is Pores with Pore children, and Paths with Path respectively.


General shape of the XML:

<Cavities Version="">
  <Cavity Type="Cavity" Volume="3589.534" Depth="20" Id="1">
      <Residues>LEU 47 A,ILE 50 A,LEU 51 A,TYR 53 A,HIS 54 A,GLN 78 A,GLN 79 A,PRO 107 A,GLY 109 A,VAL 111 A,LYS 115 A,ILE 120 A,GLU 122 A,LYS 173 A,ASP 174 A,LYS 208 A,LEU 211 A,ARG 212 A,LEU 216 A,LEU 221 A,PRO 227 A,ILE 230 A,GLU 234 A,TYR 307 A,GLU 308 A,LEU 482 A,GLN 484 A,PRO 485 A,PRO 488 A</Residues>
      <Properties Charge="0" NumPositives="4" NumNegatives="4" Hydrophobicity="-0.31" Hydropathy="-0.42" Polarity="9.84" Mutability="71" />
      <Residues>PHE 57 A,ASP 76 A,VAL 81 A,ASN 104 A,ARG 105 A,ARG 106 A,PHE 108 A,SER 119 A,ALA 121 A,GLY 177 A,MET 181 A,ILE 184 A,THR 207 A,PHE 213 A,ASP 214 A,PHE 215 A,PHE 220 A,ILE 223 A,THR 224 A,PHE 241 A,ILE 301 A,PHE 302 A,ILE 303 A,PHE 304 A,ALA 305 A,THR 309 A,SER 311 A,SER 312 A,SER 315 A,PHE 316 A,TYR 319 A,ILE 369 A,ALA 370 A,MET 371 A,ARG 372 A,LEU 373 A,GLU 374 A,ARG 375 A,VAL 376 A,VAL 393 A,MET 395 A,ARG 440 A,ILE 443 A,LEU 475 A,GLY 481 A,LEU 483 A,VAL 489 A,HEM 508 A</Residues>
      <Properties Charge="2" NumPositives="5" NumNegatives="3" Hydrophobicity="-0.18" Hydropathy="0.30" Polarity="6.29" Mutability="83" />
    <Properties Charge="2" NumPositives="9" NumNegatives="7" Hydrophobicity="-0.23" Hydropathy="0.03" Polarity="7.64" Mutability="78" />

Channels with Charges

XML output for XML channels is the same as without charges, except that the <Node> contain an additional attribute Charge:

  <Node Radius="1.556" FreeRadius="1.556" T="0.00000" Distance="0.000" X="-25.007" Y="-25.093" Z="-14.627" Charge="0.033" />

In addition to this, the XML representation of the tunnel surface is available in the form:

<Surface TotalValue="-1.268">
    <Vertex Id="0" X="-32.048" Y="-29.039" Z="-17.561" Value="0.349" />
    <Vertex Id="1" X="-32.019" Y="-28.874" Z="-17.561" Value="0.341" />
    <Vertex Id="2" X="-32.113" Y="-29.039" Z="-16.705" Value="0.177" />
    <Triangle A="2" B="3" C="0" />
    <Triangle A="0" B="3" C="1" />
    <Triangle A="4" B="3" C="2" />

Start Points

Contains the XML description of automatically computed and user added start points.


There are two types of PDB output:

  • Profile: This is roughly equivalent to <Node> elements in the XML output. The shape of the file looks like this:
REMARK ATOM  NAM RES   TUNID     X       Y       Z    Distnm RadiusA 
HETATM    1  X   TUN H   1     -25.007 -25.093 -14.627  0.00  1.56              
HETATM    2  X   TUN H   1     -24.999 -25.066 -14.700  0.08  1.60              
HETATM    3  X   TUN H   1     -24.992 -25.038 -14.773  0.16  1.65         

Each channel has its individual PDB file + a single PDB file for each channel type containing all of them.

  • Structure: Contains residues (atoms) that form the tunnel lining.


This type of output is equivalent to <Node> elements in the XML output. For charges, there is an extra column present with the charge value.


There are two types of the PyMol output:

  • Standard: Contains Channels and Cavities.
  • Charges: Contains Channel surfaces colored by charge potential (min charge = red, 0 charge = white, max charge = blue) and surfaces colored by centerline potential.

To run the PyMol output, use the "File -> Run..." option in PyMol.


Mesh files containing vertices and triangles. These files can be opened in JMol.

A JMol script to open these files might look like this:

var proteinFile = "1TQN.pdb";
var tunnelsFolder = "output\\mesh\\";
var nTunnels = 3;

load @{proteinFile};
select all; spacefill off; wireframe off; cartoons;
color blue; 

var colors = ['aliceblue','antiquewhite','aqua','aquamarine','azure','beige','bisque','blanchedalmond','blue',
  'blueviolet','brown','burlywood','cadetblue','chartreuse','chocolate','coral','cornflowerblue', 'cornsilk',
for (var i = 1; i <= nTunnels; i++) {
  pmesh ID @{i} @{tunnelsFolder + "tunnel_" + i + ".mesh"};
  color pmesh @{colors[i]};