Module: Generate Molecular Surfaces ()
This module computes molecular surfaces. Three types of molecular surfaces can be generated: the van der Waals (vdW) surface, the solvent accessible surface (sas), and the solvent excluded surface (ses). The vdW surface encloses all van der Waals spheres of the molecule's atoms. The sas encloses all van der Waals spheres extended by some probe radius. Finally, the ses encloses the subspace which is not accessible to a probe sphere in the presence of the molecule represented by its van der Waals spheres.
The implemented algorithm allows the computation of the full molecular surface as well as of partial surfaces. If the partial surface option is selected, the surface will only be computed for all highlighted atoms (see, e.g., the description of the Molecule Selection Browser). This module will register itself at the Selection Browser, which allows you to restrict the computation of the molecular surface to a subset of its atoms. For example, if the molecule consists of several chains, you can compute the molecular surface of a single chain by deselecting the other chains.
Apart from the option to compute either the full or a partial surface, you can also choose between two algorithms that differ in the quality of the surface generated, and also in speed. If time does not matter, you should always use the default option, correct. However, if you are interested in the dynamic behavior of the molecular surface, time does matter and you might want to use the second algorithm. This algorithm works as follows. We start with an arbitrary atom contributing to the surface. For this we compute the atom's surface contribution. All atoms adjacent to this atom's surface are stored in a list. Next, we take the first atom from the list and deal with it in the same fashion as for the very first atom. Thus, in the case of a vdW surface or an sas we end up with the same surface as with the correct algorithm if the surface consists of one component. In case of the ses we run into problems if two components are further away from each other than the probe's diameter. Furthermore, the faster algorithm might not compute all cavities, whereas the correct algorithm will.
A maximum of two molecules may be connected to the module, thus enabling the surface computation of a complex consisting of two molecules. This can be interesting, for example, if you want to compute the surface before and after a docking.
As a result of the computation a new object, i.e., the molecular surface, will appear in the Project View. To visualize the surface, attach the Molecule Surface View module to it.
Press the Apply button to start the computation.
Molecule [optional]
The molecule for which the molecular surface should be computed.Molecule2 [optional]
If you want to compute the surface of a complex of two molecules, you must connect this port to a second molecule.Either of those two ports needs to be connected to some molecule in order to compute a molecular surface.
Surface Type
Choose between van der Waals, solvent accessible, and solvent excluded surface. \Filter Options
Allows common filters to be applied in addition to the filtering in the MolSelectionBrowser. The option ignore waters will remove all oxygens and hydrogens which are not bonded to another heavy atoms from the computation. The option ignore het ignores all HET groups (as defined in a pdb file).
Surface Options
Quality
The default option computes the molecular surface correctly, i.e., with all, possibly disconnected, components and all enclosed cavities. The second algorithm is faster because it does not compute the molecular surface contribution for each atom, but only for surface atoms. If the surface is not connected, it might miss parts of the surface.Edge length
Choose the approximate edge length of the surface's triangles. This port corresponds to the number of points per , and vice versa. Thus, if you modify the value of this port, the value of the other port will be changed too.Number Of Points Per A^2
With this port you define the approximate number of points per and thereby the granularity of the surface.Options
If the option partial surface is selected, only the surface of the currently highlighted atoms will be computed. The second option, which is only active if the first option is checked and the surface type ses is selected, initiates the computation of the highlighted atom's adjacent patches, i.e., toroidal and spherical concave patches.Surface Area
If either the first or the second option is selected, the exact size of the current molecular surface will be computed and the size per atom or per residue, respectively, will be written to the molecules topology. For the respective level, i.e., atoms or residues, you will find a new attribute area, which contains the contribution of each item to the overall surface area. This allows you to color the molecule according to the surface contribution. It further enables you to select all surface atoms or residues (see atom expressions for details). If the last option is selected, a text field will appear allowing you to specify an arbitrary name for the attribute into which the surface areas will be written.Attribute Name
Specify an attribute name here, if you do not want to save the surface area in the attribute area. In order to do so, the third option of the Surface area port must be selected.
Radius Options
Type
The radius option determines the basic radius of the van-der-Waals spheres for which the surface is computed. When 'const' is selected, a value of 1 will be used. For 'attribute' the radius is determined by the attribute given in 'radius attribute'. Then, for different force fields there exist different radii. 'standard vdW' refers to the original standard vdW radii. 'mmff vdW' are the van der Waals radii according to the Merck Molecule Force Field (mmff).Radius Attribute
Radius value needs to be specified when attribute option is selected with radius port. This option is only available when 'attribute' option is selected with the raduius port.Atom Radius Scale and Offset
The radius of each atom as it is used in the molecular surface computation is the default atom radius as determined by the 'radius' port, scaled by the 'atom radius scale' with an 'additional atom radius' offset that is added at the end.Probe Radius
The radius of the solvent probe sphere. This port is only visible for the surface types sas and ses.