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.