PLUTON Manual

Introductory Example

The following example, of the structure of CYTOSINE should provide a simple introduction to the use of the program and its potential. The structural parameters will reside on a disk file, called name.SPF, for which the contents are listed below.

NOTE: In the WinGX implementation, this file is created automatically from the requisite model file by calling the PLUTON menu item from the GRAPHICS menu.

   TITL CYTOSINE (ANHYDROUS) ACTA CRYST. B29, 1234, 1973.
   CELL 13.044 9.495 3.814 90 90 90
   SPGR P212121
   N1   0.0222 0.0285 0.4410
   C2   -.0164 0.1561 0.3276
   O2   -.0998 0.1595 0.1710
   N3   0.0402 0.2745 0.3877
   C4   0.1308 0.2635 0.5492
   N4   0.1842 0.3828 0.5967
   C5   0.1705 0.1337 0.6674
   C6   0.1134 0.0187 0.6084
   H1   -.013  -.057  0.363
   H3   0.154  0.463  0.541
   H4   0.248  0.378  0.652
   H5   0.237  0.128  0.796
   H6   0.132  -.078  0.69

After calling PLUTON from the menu, the .SPF file is loaded and, since this file does not contain an END instruction at the end of the file, the program comes, after that the end-of-file has been reached on this file, with the prompt >>, ready to receive additional data and/or instructions interactively. When in response to the prompt the instruction PLOT is typed, the program will automatically assemble a unique molecule (i.e. symmetry operations will be applied when necessary to find connected sets of atoms), find all bonds and generate a minimum overlap stick-style plot of the structure, optionally followed by a beep signal on completion of the plot.

The program now waits for the user to press the RETURN (or ENTER) key to present the prompt >> again and to accept new instructions. Alternatively, a new instruction may be typed directly without waiting for the prompt. At this point the minimum overlap view direction may be modified with any of the available VIEW instructions.

As an example we can rotate the structure clockwise by 45 degrees about the horizontal X-axis with the instruction

        VIEW CURRENT XROT 45
        and see the effect with a new
        PLOT instruction.

The style of the plot may be changed into the SOLID, STRAW, ROD or CPK style with corresponding instructions:

        e.g. ROD SHADE followed by PLOT
        or CPK NET followed by PLOT.

A PLUTON session thus involves a series of cycles, each of which consists of contents, style and viewpoint modification instructions, if any, followed by a PLOT instruction. As an aid, it is possible to inspect the contents of the various internal tables with instructions such as LIST ATOMS, LIST BONDS or LIST ARU. On-line information on the available instructions is available by typing HELP. A status line reports the current values on some of the more relevant settings. Use HELP GRAPHICS for instructions to change the default graphics settings.

The input set of fractional coordinates from the model file is not required to form a connected set or even a complete molecule in case of molecules sitting on a crystallographic symmetry element. Unless instructed explicitly by the user, the necessarily calculations are carried out automatically as communicated to the user by the expression

        AEX:: JOIN RADII UNIQUE EXPAND.

This will automatically generate a connected set based on standard covalent radii and symmetry expanded when applicable. Where appropriate the user is informed about problems, new parameter values and the current status of relevant parameters. Intermolecular hydrogen bonds of the type Donor-H...Acceptor may now be generated with the instruction:

        JOIN HBONDS
        An alternative would be
        JOIN RADII INTER  H 1.2 O 1.5 N 1.5

but this will generate many unwanted additional contacts that will have to be deleted subsequently from the bond list). The list options (e.g. LIST ATOM, LIST BONDS or LIST ARU) may be used following this instruction to verify that several items were added to the atom, bond and aru lists. A SOLID type packing diagram with the unit cell outline and viewed down the c-axis of the structure is generated with a few additional instructions:

        SOLID
        PACK RANGE -0.5 1.5 -0.5 1.5 0 1
        UNITCELL
        VIEW ZO
        PLOT

IMPORTANT: To finish the program properly, the instruction END must be issued. If the PLUTON dialog and graphics windows are closed without this instruction, the WinGX program will stop, and need to be reloaded.

The trailer listing file provides a detailed log of the current session. All instructions are saved on a journal file to reconstruct previous style and orientation settings. In addition the name of the generated meta file (if any) is given.

NOTE: in the WinGX implementation, a dialog box appears at the end of a run, asking the user whether they should be saved.