a convenient feature for the browsing of structures that are retrieved from the Cambridge
Structural Database. In that case, an interactively supplied END statement will not stop
program execution but will load the next data set (use the instruction STOP or EXIT for
premature abortion). Facilities are available (the SAVE instruction) to run the same set of
instructions on a file that contains more than one data set (e.g. a series of structures
extracted from the Cambridge Structural Database).
3.2 – An Introductory Example
The following example, assumed to run on a unix system, of the structure of CYTOSINE
should provide a simple introduction to the use of the program and its potential. X-Window
based implementations support both keyboard instructions and menu driven input with an
automatic redraw of an updated image.
The structural parameters are assumed to reside on a disk file, named
cyto.spf in this
example, for which the contents are listed below (free format). This particular input format
is convenient for viewing structures with parameters taken from a publication:
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 0.692
PLUTON may be invoked for this data set with the command:
pluton cyto.spf
As a result the data set CYTO 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 we now type in response to the prompt the instruction PLOT, 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. 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 automatic 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
(or to the same effect 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 COLOR followed by PLOT or CPK GLOBE
COLOR followed by PLOT.
A PLUTON session thus involves a series of cycles, each of which consisting 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 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 (
Fig. 4
):
SOLID
PACK RANGE -0.5 1.5 -0.5 1.5 0 1
UNITCELL
VIEW ZO
PLOT
To finish the program the instruction END should be issued. 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.
3.3 - On How it Works
This section on program internals should provide a framework to understand most of the
effects of the available instructions. The input atomic coordinates (x, y, z) are with reference
to user- defined axes (a, b, c), which will usually be either crystallographic unit cell axes or
an arbitrary orthogonal set; these coordinates are input as fractions of the unit cell edges or
as Angstrom units (in the latter case they are converted to and stored internally as fractions