Display Menu

Surface Area and Volume: Calculate Surface area of molecule using Connolly algorithms.

Assign Point Group: Assign point group symmetry.

Compare: Compare different structures.

Dihedral Plot: Display the results of dihedral driver calculations.

Movie: Replay of all the structures in a multiple structure file

Dot Map: Generate a dot map from a multi conformation file

Multi Strucutre File: Analyze a file containing multiple structures

Orbitals: Display molecular orbital data

IR Spectra: Display Frequency data and animate vibrational mode.

Surface Area and Volume

This option calculates the surface area and volume of the current molecular system analytically using the algorithms published by M. Connolly (M. L. Connolly, "Analytical Molecular Surface Calculation", Journal of Applied Crystallography, 16, 548-558 (1983) and M. L. Connolly, "Computation of Molecular Volume", JACS, 107, 1118-1124 (1985

Assign Symmetry

This option attempts to assign the point group of the current structure using the cartesian coordinates. If successful the point group and the moments of inertia are reported.

Compare

This option allows the comparison of two or more structures. The main structure is, by definition, the structure with the lowest molecule number. A dialog box is presented in the Template Window to control the options and any structures present are colored by their molecule number. The options in the Compare Dialog are:

Compare By:

Non-volatile atoms : compare two structures using all non-volatile atoms (everything but hydrogens attached to carbon)

Selected Atoms: compare using the selected atoms as setup below

Moments of Inertia: compare by moments of inertia. Will see chiral structures as identical.

Control Buttons

Calculate: do a comparison of two structures using a least squares calculation to minimize the difference in the positions of the atoms being compared. The structures are redrawn in the best overlapped positions.

Next Str: Read in the next structure for comparison. The main structure and the new structure will be displayed and any other previously compared structures will be hidden.

Show/Hide: Control the display of multiple structures. Dy default only two structures are shown at any time, but this can be changed to show some or all of the overlapped conformers. Useful for generating a picture/graphics image of the overlap.

Selected Atom Setup

Update Sel Atoms 1 / Clear Sel Atoms 1: read the atoms selected with SELA from the main structure and save this information. Display the atom number in the edit box. Clear the selected atoms so a different set may be chosen.

Update Sel Atoms 2/ Clear Sel Atoms 2: read the atoms selected with SELA from the higher numbered molecule and save this information in the edit box. This set of atoms will be used for subsequent structures on the assumption all the structures are conformers.

Comparison Results:

The structures are compared atom by atom. The average difference, the Rms difference and the atom by atom differences are reported. 

Done – ends the Comparison dialog. All comparison structures are deleted, and the main structure is re-displayed.  It is necessary to erase all the comparison structures since they occupy the same coordinates as the main structure (if the comparison has been successful), and would cause any subsequent molecular mechanics to fail. 

Dihedral Plot

This option allows redisplay of the results of a prior dihedral driver calculation. A dialog box is presented prompting for the filename of the saved calculation. The file is then read and a one angle or two angle plot is presented. See the FILE OPEN command for a detailed discussion of the use of the file dialog box, and the DIHEDRAL_DRIVER option in the Display Menu for a full discussion of dihedral driver calculations.

Movie

This option brings up the Movie Template. The purpose of the Movie player is to read a multiple structure file and play the structures in sequence simulating a movie. The filet types currently supported include: Pcmodel, SDF, Mol2, XYZ, CML, Gaussian log file, Gaussian IRC, Mopac AUX and DRC, Gamess output, and Lammps Dump File. The options in Movie dialog box are:

Structure Number/Progress Bar: The number of structures in the file and the current structure being displayed.

Play – Plays the movie and updates the Structure Number and Progress Bar.

Step – Steps through the file one structure at a time.

Loop – Continuously plays the movie.

Stop – Stops the Play or Loop.

Create AVI Movie: Play the movie and write a graphics file (png format) at each step. At the end the graphics files can be combined into an AVI format movie using FFMPEG or MENCODER.

Create a PovRay Movie: Play the movie and write a PovRay input file at each step. Then use Movie option in PovRay to render each file and then combine them to form a movie.

Keep Movie Intermediate Files: Keep the PNG or PovRay input files after the Movie is run in case FFMPEG or MENCODER fails to run from within Pcmodel.

Open Structure File: Bring up a File Open dialog to get the name of the file of structures to play.

Dot Map

This option reads in a file from a Conformational Search, compares a selected set of atoms and orients each structure to overly the first structure, then plots the position of a selected atom from each structure relative to the original structure. The result is a new structure containing the position of every place where the selected ‘dot’ atom can visit in the various conformations.  See Midland, M.M.; Plumet, J.; Okamura, W.H. “Effect of C20 Stereochemistry on the Conformational Profile of the Side Chains of Vitamin D Analogs,” Bioorganic and Med. Chem. Letters 1993, 3, 1799-1804. for an application in the vitamin-D field. 

After selecting Dot Map, a file open dialog box will appear. Usually you will want to use the first structure for the comparison. Use SELA to select the atoms for structure comparison and overlay then hit Update Selected Atoms. Next select the atom for the dot again using SELA.

MultiStructure

View Structures.  The View structures option provides a quick way to step through a file and look at individual conformations. A scrolling list of all the structures in the file is shown and the file is displayed when selected from the list. This is very similar to a standard file open, but the scrolling dialog box is not dismissed and no questions are asked.

Orbitals



IR-Spectra