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3. Mapping molecules

User interface

The interface of the structure mapping tool is divided into two main parts: the molecule visualizer and the controls below it. The visualizer displays a 3D representation of the molecule and allows one to rotate, translate or zoom the molecule.

Basic mouse operations:
To rotate a molecule: click and drag.
To translate a molecule: SHIFT + double click and drag.
To zoom a molecule: SHIFT + click and drag vertically.

More operations are described in the Jmol mouse manual: http://wiki.jmol.org/index.php/Mouse_Manual

Controls are divided into Molecule, Weights, Beads, Bonds, Angles, Dihedrals and XML sections. The Custom section allows you to pass Jmol commands directly to the visualizer. Sections are organized into tabs. Clicking on tabs switches sections.

Molecule section

In the Molecule section, you upload a molecule file. Any file format supported by Jmol may be used (see Jmol file formats). The molecule is displayed in the visualizer after upload. In this section you also enter the molecule name and ident. These are the names of the molecule in the coarse-grained and atomistic representation, respectively.

Weights section

In the Weights section, you define the weight mappings from atomistic to coarse-grained representation. Since the weights of atoms are known, this process can be done automatically while defining beads, if the Automatically map weights option is checked.

If for some reason you whish to define the weights manually, this can be done by entering the weight name and its corresponding atom weights. Atom weights should be separated by space in descending weight order. STOCK will also try to order the atoms of a bead by weight descending. In the XML file, the order of the atoms in a bead, and their weights in the corresponding map should match.

When a weight is added, it appears in the list on the right. A weight may be removed by selecting it and clicking the Remove button. If the weight is in use by some bead, it cannot be removed (the bead must be removed first).

Beads section

In the Beads section, you define beads by clicking atoms in the visualizer (beads are coarse-grained particles which are used in coarse-grained simulations replacing a group of atoms). The bead name, type and mapping can be set. The weights map is disabled in case of automatic mapping of weights. Bead name is usually a letter followed by a number. For your convenince, STOCK will automatically increase the number after a bead has been added.

Some file types also define groups of atoms. If this information is provided and Group select is enabled, clicking an atom, will select all atoms in the group. The Bead size option toggles the displayed size of the beads in the visualizer. It has no effect on the XML file.

When a bead is added, it appears in the list on the right. To see which atoms are in a bead, select it, and the corresponding atoms will be marked with a green halo in the visualizer. A bead may be removed by selecting it and clicking the Remove button. If the bead is in use by some bonds, angles or dihedrals, those will also be removed.

Bonds section

In the Bonds section, you define bonds by selecting the corresponding two beads in the drop down menus. A custom bond name may be entered. The currently selected bond is displayed in the molecular visualizer in yellow. The already added bonds are blue.

When a bond is added, it appears in the list on the right. A bond may be removed by selecting it and clicking the Remove button.

Angles section

In the Angles section, you define angles by selecting the corresponding three beads in the drop down menus. A custom angle name may be entered. The currently selected angle is displayed in the molecular visualizer in yellow. The already added angles are blue.

When an angle is added, it appears in the list on the right. An angle may be removed by selecting it and clicking the Remove button.

Dihedrals section

In the Dihedrals section, you define dihedrals by selecting the corresponding four beads in the drop down menus. A custom dihedral name may be entered. The currently selected dihedral is displayed in the molecular visualizer in yellow. The already added dihedrals are blue.

When a dihedral is added, it appears in the list on the right. A dihedral may be removed by selecting it and clicking the Remove button.

XML section

In the XML section, the XML code defining the current configuration is displayed. You may download the code as a file, or copy it to your clipboard, which may then be pasted to any text editor. The generated XML file is readily used as the input topology file for VOTCA or DL_CGMAP package. The Switch to Boltzmann button will open STOCK: Boltzmann inversion tool, and show a list of pair potentials that have to be generated for this molecule.

Custom section

In the Custom section, you may pass custom JSmol/Jmol commands to interact with the displayed molecule. Some examples are provided in the tooltip that appears when you click in the text field. A complete list of commands with examples is provided in the JSmol/Jmol documantation: http://chemapps.stolaf.edu/jmol/docs/.



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