Mole 2.5 Command Line Input Help

General XML input shape

<Tunnels>
  <Input Attributes="...">filename</Input>
  <ChargeSources>
    <ScalarGrid Attributes="..." />
    <AtomValues Attributes="..." />
    <RandomGrid Attributes="..." />
    <!--More optional Field elements-->
  </ChargeSources>
  <WorkingDirectory>path</WorkingDirectory>
  <Params>
    <Cavity Attributes="..." />
    <Tunnel Attributes="..." />
    <Filter>MotiveQuery expression (see http://webchem.ncbr.muni.cz/Wiki for help)</Filter>
  </Params>
  <Export>
    <Formats Attributes="..." />
    <Types Attributes="..." />
    <Mesh Attributes="..." />
    <PyMol Attributes="..." />
  </Export>
  <CustomVdw>
    <Radius Element="C" Value="1.75" />
    <!--More optional Radius elements-->
  </CustomVdw>
  <NonActiveResidues>
    <Residue SequenceNumber="123" Chain="A" />
    <Query>MotiveQuery expression (see http://webchem.ncbr.muni.cz/Wiki for help)</Query>
    <!--More optional Residues or Query elements-->
  </NonActiveResidues>
  <CustomExits>
    <Exit>Point specification</Exit>
    <!--More optional Exit elements-->
  </CustomExits>
  <Origins Auto="0 or 1">
    <Origin>Point specification</Origin>
    <!--More optional Origin elements-->
  </Origins>
  <Paths>
    <!--Optional-->
    <Path>
      <Start>Point specification</Start>
      <End>Point specification</End>
    </Path>
    <!--More optional Path elements.-->
  </Paths>
</Tunnels>

Point specification

Points can be specified in 4 ways:

One or more residue elements: <Residue SequenceNumber="123" Chain="A" InsertionCode=" " />
One or more 3D points that 'snaps' to the closest residue: <ResidueFromPoint X="1.0" Y="2.0" Z="3.0" />
One or more 3D points: <Point X="1.0" Y="2.0" Z="3.0" />
MotiveQuery expression (see http://webchem.ncbr.muni.cz/Wiki for help): <Query>expression</Query>; Creates a point from each motif returned by the query.

The final start point is defined as the centroid of atomic centers or defined points.

Parameter Descriptions

Types

[string] - a sequence of characters

[real] - a floating point number (1.23)

[int] - an integer (123)

[bool] - 0/1 or True/False

<Input> attributes

SpecificChains [string], Default value = none

One or more characters that specify which chains should participate in the computation. If empty or non present, all chains are loaded.

ReadAllModels [bool], Default value = False

Determines whether to read all models from the PDB file. All models are read automatically for PDB assemblies (.pdb0 extension).

<ChargeSources> elements

<AtomValues> attributes

Name [string], Default value = none

Name of the field.

Source [string], Default value = none

Filename of the source. Supported formats: OpenDX.

Method [string], Default value = NearestValue

Method used for charge computation [NearestValue, RadiusSum, RadiusSumDividedByDistance, RadiusMultiplicativeScale, RadiusAdditiveScale, KNearestSum, KNearestSumDividedByDistance, Lining, WholeStructure].

Radius [real], Default value = 5

Radius used for the Radius* methods.

K [int], Default value = 5

Number of neighbors used used for the KNearest* methods.

IgnoreHydrogens [bool], Default value = False

Determines if to consider hydrogens for value assignment.

<RandomGrid> attributes

Name [string], Default value = none

Name of the field.

MinValue [real], Default value = -1

Minimum value to generate.

MaxValue [real], Default value = 1

Maximum value to generate.

<ScalarGrid> attributes

Name [string], Default value = none

Name of the field.

Source [string], Default value = none

Filename of the source. Supported formats: OpenDX.

<Params> elements

<Cavity> attributes

IgnoreHETAtoms [bool], Default value = False

Allows to exclude the HET atoms from the calculation.

IgnoreHydrogens [bool], Default value = False

Allows to exclude the hydrogen atoms from the calculation.

InteriorThreshold [real], Default value = 1.25

Minimum radius of void inside the protein structure, so that the void would be considered a cavity.

MinDepth [int], Default value = 8

Minimum cavity depth in the number of tetrahedrons.

MinDepthLength [real], Default value = 5

Minimum depth of a cavity in angstroms.

ProbeRadius [real], Default value = 3

Regulates level of detail of the molecular surface. Higher Probe Radius produces less detail.

<Tunnel> attributes

AutoOriginCoverRadius [real], Default value = 10

The minimal distance between two auto origins in a given cavity.

BottleneckRadius [real], Default value = 1.25

Minimal radius of a valid tunnel if BottleneckLength is 0.

BottleneckTolerance [real], Default value = 0

Maximum length of a valid tunnel for which the radius is less than Bottleneck Radius.

FilterBoundaryLayers [bool], Default value = False

Determines whether to remove layers with boundary residues from the tunnel.

MaxAutoOriginsPerCavity [int], Default value = 5

The maximum number of automatically computed origins per cavity.

MaxTunnelSimilarity [real], Default value = 0.9

Maximum degree of similarity between two tunnels before one tunnel is discarded.

MinPoreLength [real], Default value = 0

Determines the minimal length (in ang) of a pore.

MinTunnelLength [real], Default value = 0

Determines the minimal length (in ang) of a tunnel.

OriginRadius [real], Default value = 5

If the user defined a tunnel start point, expand the search for tunnel start points to a sphere of radius.

SurfaceCoverRadius [real], Default value = 10

Regulates the density of exit points tested at each outer boundary. Higher Surface Cover radius produces a lower density of exit points.

UseCustomExitsOnly [bool], Default value = False

Only user defined exits are used for tunnel computation.

WeightFunction [string], Default value = VoronoiScale

Determines the weight function used to compute channels [VoronoiScale, LengthAndRadius, Length, Constant].

<Filter> element

A MotiveQuery lambda expression that returns True to keep the given channel or False to discard it.

<Export> elements

<Formats> attributes

ChargeSurface [bool], Default value = True

Controls if XML representation of surface with charges is created.

CSV [bool], Default value = False

Controls if CSV export or channel profiles created.

Mesh [bool], Default value = False

Controls storing information about the mesh of detected tunnels, for subsequent visualization in PyMol or Jmol.

PDBProfile [bool], Default value = False

Controls if channel profiles are exported in PDB format.

PDBStructure [bool], Default value = False

Controls if channel residues (surrounding atoms) are exported in PDB format.

PyMol [bool], Default value = False

Controls whether a PyMol script will be generated, for subsequent visualization in PyMol.

<Mesh> attributes

Compress [bool], Default value = False

Controls storing of mesh information in a GZip file archive.

Density [real], Default value = 1.33

Level of detail of mesh surface. The higher the Mesh Density, the lower the level of detail in the visualization.

<PyMol> attributes

ChargePalette [string], Default value = RedWhiteBlue

Determines the palette used for charge coloring [RedWhiteBlue, BlueWhiteRed].

PDBId [string], Default value = none

If this value is present, the option for downloading the structure is incorporated in the PyMOL visualization script.

SurfaceType [string], Default value = Surface

Controls, if channels are displayed in PyMOL as isosurface or as a set of spheres [Surface, Spheres].

<Types> attributes

Cavities [bool], Default value = True

Controls whether cavities will be exported.

PoresAuto [bool], Default value = False

Controls whether 'auto' pores will be computed.

PoresMerged [bool], Default value = False

Controls whether merged pores will be computed.

PoresUser [bool], Default value = False

Controls whether user exit pores will be computed.

Tunnels [bool], Default value = True

Controls whether tunnels will be computed.

<Origin> attributes

Auto [bool], Default value = False

Determines whether to (also) use automatically computed tunnel start points.