Chapter 10 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 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
Assign Sym Assign point group symmetry.
This option calculates the exposed surface area of the current molecular system. A stochastic algorithm is used which generates points on the surface randomly, determines if the point is exposed or not, and counts the number of exposed and unexposed points. A dialog box is used to set the number of points calculated for each atom (default 100), and the number of times the calculation is repeated (default 20). Since the method is stochastic the calculation is normally repeated several times and the average surface area values are reported. The calculation may be aborted by pressing the ESC key.
When the calculation is complete, a window will appear with the total surface area, saturated area, unsaturated area and polar area. (The atom types of the atoms are used to divide the surface into non-polar, unsaturated non-polar and polar surface areas.)
This option calculates the volume of the current molecular system. Both molecular volume (in cubic Å) and molar volume (in cubic cm) are reported. The calculation may be aborted by pressing the ESC key.
This option allows the comparison of two or more structures. The main structure is, by definition, the structure with the lowest substructure number. If only one structure is present when the Compare option is first selected, the structure is redrawn colored by substructure and a dialog box is displayed so that a comparison structure can be read in. If two or more substructures are present when COMPARE is selected, the structures are redisplayed colored by substructure and the compare dialog box is then displayed.
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Comparisons can be done an all atoms (default), heavy atoms only, or selected atoms only. In order to use the Selected atoms option, the atoms must be SELECTed using the SELECT button from the TOOLS menu before the COMPARE option is chosen. The atoms may be marked in any order, but the calculations will match the first selected atom of one structure with the first selected atom in the second structure, and so on. Alternatively, one atom in the first structure may be selected, followed by the atom to be matched to it in the second structure.
The other option in this dialog box are:
Calculate - starts a least squares calculation which attempts to minimize the differences in the positions of the atoms being compared. The results of the calculation will be given in the Compare window. The table of results will include 3 columns - atom in structure 1, corresponding atom in structure 2, and distance between them in angstroms. At the bottom of the table are the average difference between the distances, and then the root mean square difference in the distance. If the output is too large to fit in the window, the window can be scrolled. The structures will be drawn in the Structure window overlapped with red lines connecting the atoms that are being compared. If the structures overlap well, the red lines may not be visible.
Reset - clears the comparison arrays and removes the red lines between comparison atoms from the drawing. This button is essentially used only for cleaning up the screen.
Next Structure - allows reading in another structure for comparison. If two or more structures are currently present, all but the main comparison structure will be hidden. a file dialog box will be presented for selecting the desired structure file, the structure will be read in and displayed to the right of the current structure, colored in the appropriate substructure color.
Hide - makes all the comparison structures invisible. This is useful to keep the screen from becoming cluttered when many structures are being compared.
Show All - makes all comparison structures visible. This is useful to display several structures that have been compared.
Cancel - dismisses the Compare dialog box. 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.
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 ANALYZE menu for a full discussion of dihedral driver calculations.
This option reads a multiple
structure file and shows all the structures in sequence. The file formats
currently supported include PCM, MMX, Gaussian output and Cambridge Structural
Database. PCM type multiple structure files are often generated during a
dynamics run, or part of a GMMX search. Thus the results of a dynamics run can
be replayed using this options. Another use of this option is to view the
results of a Gaussian reaction coordinate scan. You will first be asked to select a file for
play. The options in this dialog box
are:
Play – Plays the movie.
Step – Steps through the file one structure at a time.
Loop – Continuously plays the movie.
Stop – Stops the Play or Loop.
Exit - Exits the dialog box and returns to PCMODEL.
The total number of structures in the file (5 in the illustration) and the current structure number (1) will be displayed. The track bar reports the progress of the movie but does not respond to clicks of the mouse.
This option reads in a file from a
GMMX 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-read dialog box will appear. Usually you will want to use the first
structure for the comparison. Next enter
the atom numbers for the comparison overlay.
This can be done by either typing in the numbers separated by a space or
comma, or by using the Sel-Atm option from the Draw Tools. If Sel-Atm is used, click on Update to fill
in the edit box. Next select the atom
for the dot. This can be done by
entering an atom number or by reselecting Sel-Atm, clicking on the appropriate
atom and then on Update. The dots will
look bigger on the screen then in the print out. Do not add hydrogens to the resulting
structure, particularly if the dot atom is an oxygen or nitrogen. An example of a dot map is shown below.
Multi structure/conformation files can be analyzed. There are three main options- View Structures, Analyze Structures and Compare and Extract Structures.
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.
Analyze Structures. This option allows you to perform query
operations (distance, angles etc) as well as surface area, volume and box size
calculations on a multi structure file.
Clicking on the Query buttons will provide a dialog box for editing the
query list. Queries may be entered by
using the Query button from the DrawTools and then hitting the Update Queries
button. If the multi structure file is
from a GMMX search, then the energy information will be read from the file and
used to calculate a Boltzmann distribution for the queries. You will be asked to give the name of an
output summary file.
Compare
and Extract Structures. This option
allows you to compare all structures in a file or in two files, To extract all structures which
match a query or to extract a set of structure from a file. For example you may want to retrieve all
structures from a GMMX search which have two atoms 5.1+/-0.3 A apart
This option attempts to assign the point group of the current structure using the cartesian coordinates.