File Menu
Open Reads a file from disk.
Save Saves a file to disk
SaveGraphic Saves a graphics image to a disk file
Print Prints the current structure and energy windows
Read pcmod.bak Read pcmod.bak file
Exit Exits PCMODEL
Edit Menu
Draw Recovers the TOOLS menu
Erase Erases all structures
Structure Name Edit or enter name of current structure
Hide Hydrogens Make the hydrogens in a structure invisible but still present
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 a structure.
Retype Forces PCMODEL to reassign atom types.
Copy_To_Clipboard Copies an image of the structure window to the clipboard.
Orient_XY Orients the selected three atoms in the XY Plane with the Orient_XZ first atom at the origin the second atom along the axis and the Orient_YZ third atom in the plane.
Build Solvent Box/Solvate Build a box of solvent molecules or solvate the current structure.
Build Periodic Box Build a box of the current structure.
View Menu
Control Panel Brings up a dialog box to scale, translate and rotate structures in the structure window.
Labels Brings up a dialog box to change the structure labels
Mono/Stereo Toggles between mono and stereo display
Stick Figure Display all structures as stick figures.
Ball and Stick Display all structures as ball and stick.
Pluto Display all structures as Pluto type ball and stick.
Tubular Bonds Display all structures as Tubes.
CPK Surface Display all or selected structures with CPK surface.
Dot Surface Display all or selected structures with dot surface.
Ribbon Display a Ribbon diagram of peptide or nucleic acid backbone
Wht/Black Background Sets background color
RedGreen Stereo Sets view to red/green stereo
Top View Turns on top view of current structure
Dipole Vector Draws a dipole moment vector on current structure.
Compute Menu
Minimize Minimize the current structure(s).
Single Point Calculate the energy of the current structure(s).
Use External Charges Use charges read from Mopac or Ampac file
Use Gasteiger Charges Use charges generated by Gasteiger sigma model
Normal Vibrational Modes Compute normal vibrational modes
Mopac Runs the quantum chemistry program Mopac.
Ampac Runs the quantum chemistry program Ampac
Gaussian Runs the ab initio quantum chemistry program Gaussian.
Orbitals Runs the Orbdraw program to view molecular orbitals and electron densities
Vibrations Runs the Vibrate program to view normal vibrational modes
GMMX Runs the conformational searching program on the current structure.
Metropolis MC Runs conformational search using Monte Carlo algorithm
Vibrational Mode Search Runs conformational searching using low frequency vibrational modes as search directions.
Dynam Molecular Dynamics simulation.
Auto Dock Simulated annealing search of lowest energy interaction
between two structures.
Manual Dock Manually move two structures to dock them
Batch Read a multiple structure file and minimize all structures.
Rot_E Rigid rotor evaluation of rotational energy barrier.
Dihedral Driver Grid search with minimization evaluation of rotational energy barrier.
Analyze Menu
Surface Area Calculate Surface area of molecule.
Volume Calculate Volume of molecule.
Compare Compare different structures.
Dihedral Map Display the results of dihedral driver calculations.
Movie Replay the structures contained in a multiple structure file. Currently supports PCM, MMX, Gaussian and Cambridge Structural Database file formats.
Dot Map Generate a dot map from a multi conformation file.
Multi Structure File Analyze a file containing multiple structures.
Assign Sym Assign point group symmetry to current structure.
Substr Menu
Read Read a structure file and label the structure as a substructure.
Create Label the selected structure as a substructure
Move Move the selected substructure.
Connect Connect two structures.
Erase Erase the selected substructure
Show Dummy Displays dummy atoms in current structure.
Don't Minimize Mark the selected substructure so that it will not be minimized in a molecular mechanics calculation.
Templates Menu
Rings Dialog box to read in selected ring systems.
Amino Acids Dialog box to read in and connect Amino Acids.
Sugar Dialog box to read in and connect Sugars.
Nucleosides Dialog box to read in Nucleosides.
OrganoMetallics Dialog box to read in selected organometallic structures.
Transition State Dialog box to read in selected transition state models.
Functional Groups Dialog box to read in selected functional groups for connection to larger structure.
Mark Menu
H Bonds Hydrogen Bonds
Pi Atoms Pi atoms.
Metal Coord Set electron count, charge and coordination of metal atoms.
TS_BondOrders Set the bond orders for transition state bonds.
Fix Distance Fix a distance between any two atoms-up to 10 pairs
Fix Angle Fix an angle.
Fix Torsions Fix a dihedral angle
Equivalent Pi Atoms Mark pi atoms to be made equivalent in MMX calculation.
Reset Reset any of the above and also substructure membership.
Options Menu
Printout Sets the amount of output in the output file, PCMOD.OUT.
Dielc Resets the dielectric constant.
DPDP Change between dipole-dipole and electrostatic calculations.
Minimizer Set options for the minimizers.
MMX_Pi Calc Set options for Pi calculation
Added Constants Allows user defined constants
Standard Constants Rereads the default MMX datafile
Stereo Changes the direction of rotation of stereo display.
Pluto Sets options for the Pluto Display.
VDW Surface Sets the options for the VDW display.
DOT Surface Sets the options for the DOT surface display.
Force Field
MMX Use the MMX atom types, parameters and force field.
MM3* Use the MM3 atom types, parameters and force field
MMFF94 Uses the MMFF94 atom types, parameters and force field.
Amber Uses the Amber 95 atom types, parameters and force field.
Oplsaa Uses the Oplsaa atom types, parameter and force field.
Help Menu
About Current version of PCMODEL.
Quick Summary of TOOLS Menu:
Select Select atoms.
Draw Draw a carbon skeleton in either the plane of the screen or the plane of the first selected atom.
Build Generate 3-D structure by replacing selected hydrogen with methyl group. Starting from ethane, any hydrogen selected will be replaced by methyl.
Update Update the structure and redraw the screen.
H/AD Add and delete hydrogens and lone pairs.
Add_B Increment the bond order of the selected bond.
In Push an atom into plane of screen.
Out Pull atom out of plane of the screen.
Del Delete an atom or bond.
Move Move an atom. Select Move, then atom, then new position.
Rot-B Rotate about the bond selected by four connect atoms.
Query Query selected distance, angle or dihedral. Works by first selecting Query, then selecting two, three or four atoms followed by blank space in drawing window. Queries removed by selecting Update button twice.
PT Dialog box to choose atom type.
Metals Dialog box to choose metal atom type.
Rings Dialog box to read in selected ring systems.
AA Dialog box to read in (and connect) Amino Acids.
Su Dialog box to read in (and connect) Sugars.
Nu Dialog box to read in Nucleosides.
OrgMet Dialog box to read in OrganoMetallic structures
TransSt Dialog box to read in transition state models.