The molefacture plugin provides VMD users with an interface to edit molecules. This includes the ability to add, delete, or manipulate their structure at an atomic level, and to build new components from a library of common fragments.
The current version of molefacture is still under active development, and thus several planned features are unimplemented. Fragment and peptide building is now working, although future versions will also include a nucleic acid builder and a larger fragment library. In addition, it is always possible that the program will not always make correct guesses on things like automatic hydrogen placement, although great pains have been taken to ensure that it is correct for all cases we are aware of (please contact petefred@ks.uiuc.edu if you find cases where it makes a mistake or run across other bugs). Finally, as it stands now molefacture is best suited to working on small structures (a few hundred atoms or less), although this will also be improved in future versions.
Molefacture may be invoked from the command line or through a graphical interface found under the Modeling submenu of the extensions menu. Invocation from the command line is as follows:
package require molefacture ::Molefacture::molefacture_gui $selIn either the GUI or command line mode, molefacture may be invoked with or without a selection (this should be an atomselect object on the command line, or selection text from the GUI). If a selection is provided, this selection will be loaded into molefacture; otherwise, a blank molecule will be created.
When molefacture is invoked, the main VMD display will cut to a view of the segment being edited, and the menu shown in the figure above will appear. Molefacture offers interfaces for editing atoms, bonds, and angles, as well as menus for performing general functions.
The Molefacture "File" menu offers options to save your edited molecule (as a pdb or xbgf file) or to undo all changes that have been applied since the molecule was last saved. Note that if you save your molecule as a pdb, information on charges and force field types will be lost, whereas the XBGF format (a modification of the MSI biograf format) will retain all of this information. Because molefacture is fully integrated into VMD, you may also save your edited molecule in other file formats working through the TkCon or the main VMD GUI.
The Build menu provides a number of options for construction of new molecules. The "Add All Hydrogens" button will fill out all remaining open valences in the molecule with hydrogens. Two options are available for construction of molecules from basic organic fragments, "Replace hydrogen with fragment" and "New molecule from fragment". As might be expected from the names, the former menu replaces a selected hydrogen with a small organic fragment, while the latter creates a new molecule from a small organic fragment. The Build menu also has a "Protein Builder" button, which opens a separate menu allowing the construction of short polypeptide chains.
By default, molefacture displays radicals as purple cones, lone pairs as green cones with a pair of spheres at the end, and shows the formal charge of all atoms with nonzero charges (this is not the same as the partial charge on the atom for the purposes of the MD force field). Both the display of electrons and of formal charges can be toggled in the Settings menu.
The Atoms frame displays a list of all atoms in the edited fragment, along with several important properties. In this listing, "Open" refers to the number of open valences on an atom, "FormCharge" to its formal charge, "OxState" to the number of valence electrons on the atom, and "Charge" the atom's actual partial charge (the charge that appears in a PSF, for example). Atoms may be selected for manipulation either by clicking on them in the Atoms menu or by picking them in the VMD OpenGL display. The following manipulations may be applied to atoms using this menu:
The bonds frame shows a list of all covalent bonds formed between atoms in the edited fragment. Bonds may be selected either by clicking on the list or by holding shift and clicking on two atoms int the VMD OpenGL window. Lowering a bond order to zero removes the bond, and selecting two atoms which are unbonded and then raising their bond order creates a bond between them. This frame also allows manipulation of the length of the chosen bond, or rotation of the dihedral centered on that bond (if there is one).
Similar to the atoms and bonds menus, the angles menu shows all currently formed angles in the edited fragment (an angle is defined as any set of two bonds with one atom in common). The angles frame provides a slider for changing the selected angle; angles can be picked either from the menu in the frame or by holding shift and clicking on three atoms in the VMD OpenGL window. The "Move" radiobutton allows you to pick either of the two non-central groups associated with the angle to move while scaling the angle.