Chapter 7 Edit Menu
The EDIT menu contains the following commands:
Draw Recovers the TOOLS menu
Erase Erases all structures
Structure Name Edit or enter name of current structure
Hide Hydrogens This option toggles display of hydrogen atoms on and off. The hydrogens are not removed from the structure, merely un-displayed. This allows for a much clearer drawing without changing the geometry as with H/AD.
Epimer Epimerizes the selected atom by interchanging the two selected attachments.
Enantiomer Reflects the structure through a specified axis.
Remove LP Remove lone pairs from heteroatoms.
Retype Force PCMODEL to retype the current structure.
Copy__To_Clipboard Copies an image of the structure window to the clipboard.
Orient_XY Plane Orient the molecule in a specified plane, placing
Orient_XZ Plane the first selected atom at the origin, the second
Orient_YZ Plane atom along the axis and the third atom in the
plane. Useful when generating structures for MO calculations
Build Solvent Box/Solvate Build a box of solvent molecules or solvate the current structure.
Build Periodic Box Build a periodic box from the current structure.
The DRAW option brings back the Drawing Tools buttons if they are not visible, or makes them the active window if they are visible. Otherwise, this command does nothing. The commands in this Tool bar are described in detail in chapter 5 of this manual.
This command erases the current structure and resets the default conditions for modeling. Since any unsaved structures will be lost, a dialog box appears and confirmation is required before the structure is actually erased.
This option brings up a dialog box for entering or editing the name of the current structure. The default structure name is "untitled". If a file containing a named structure is read, then the current structure name is replaced by the name from the file. The structure name is displayed in the title bar of the PCMODEL window, just to the right of the word "PCMODEL". The structure name is limited to 60 characters and will be written into the structure file whenever the structure is written to disk (if the filetype selected supports structure names).
This option toggles the display of hydrogens attached to carbon. The atoms are still present in the structure database they are just not displayed. This will often make the display less cluttered, especially if atom numbers or types are being displayed.
This option allows for inversion of the stereochemistry at a particular chiral center. Before selecting EPIMER, the central atom and the two attachments to be switched must have been selected with the SELECT command from the TOOLS menu. Once the three involved atoms have been SELECTed, the EPIMER option can be chosen and the position of the two attachments (and all atoms attached to them) will be exchanged. This option will not work if the two attachments are connected to each other in a chain.
This option allows for enatiomerization of the structure by reflecting through an axis selected by the user.
This option forces immediate removal of lone pairs from heteroatoms. Only the MMX force field uses lone pairs and lone pairs are normally removed automatically when calculations are done with any other force field. However, you may force removal of lone pairs with this option.
This option forces PCMODEL to retype the current structure.
Selecting this option copies the current structure window to the clipboard with all color information intact. The clipboard can then be copied into a paint program for editing, or it can be printed when a color printer is available.
Orient_XZ Plane
Orient_YZ Plane
These commands will orient the molecule in the selected plane. Select three atoms using the Select command from the DrawTools menu, then select one of these options. The first selected atom will be placed at the origin, the second atom will be placed along the axis and the third atom will be rotated to lie in the plane specified. This option is useful for orienting a structure before writing an input file for a molecular orbital calculation.
This option is used to build a box of solvent molecules or to solvate the current molecule. If there is molecule in the structure window when this dialog is called the dimensions of the smallest box enclosing the current structure will be calculated and displayed in the Mol Dimensions edit boxes. The default solvent is set to water but may be changed to chloroform, octane or to the current structure. The number of molecules desired must be entered and the density may be changed at this time. The cell size that is required to contain the current structure and the number of solvent molecules at the entered density is computed and displayed in the Cell Size edit boxes. Hitting the OK button will causes the solvent molecules to be added and the dialog box dismissed. If there is a current structure on the screen it will be moved to the center of the box and the remainder of the molecules will be added using the skew start method of Refson (K. Refson, Moldy v 2.9 …..). The skew start method works well for small, compact molecules whose dimensions are nearly spherical. If you want to build boxes of odd shaped molecules, those whose dimensions are elongated in one dimension, then you should use the Build Periodic Box command discussed below. Upon exiting this dialog the force field calculations are set to use Periodic Boundary Conditions for minimizations and dynamics calculations. We currently use a minimimum image convention, a spherical cutoff for dispersion interactions and a particle mesh ewald method for long range electrostatic interactions. Due to the organization of the code in PCMODEL these calculations are currently very slow and PCMODEL is probably not the program of choice for production dynamics calculations. However for short runs, initial testing and visualization PCMODEL works fine.
This menu
options is useful for building periodic boxes of oddly shaped molecules. There
must be a molecule currently on the screen for this dialog to function. The
molecular dimensions of the current structure are computed and displayed in the
Mo
l Dimensions edit boxes. The number of molecules to include in the box and the
desired density must be input. Calc Cell Size computes the cubic cell required
to hold the number of molecules at the current density. Build Cell adds the
appropriate number of molecules to the cell using the “skew start” method (see
above). The resulting cell can then be visually examined for bad non-bonded
interactions and a single point energy calculation done to assess the extent of
bad non-bonded interactions. If there are severe molecular overlaps the added
molecules can be erased using the Reset Cell button which returns the cell to
its initial state. The density can then be changed and the process of building
the cell can be repeated. By this interactive method a reasonable starting cell
can be obtained without severe non-bonded interactions. Energy minimization
followed by dynamics runs with increasing densities can be used to build a
relaxed cell at the density desired for study.