Mole 2.5 Command Line Input Help

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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.