PLUTON - MANUAL

1.0 - INTRODUCTION TO PLUTON

PLUTON is an easy-to-use interactive graphics program. It can be used as a tool for viewing, analysis and presentation of molecular structures. Drawings of either individual molecules or assemblies of molecules in a crystalline arrangement can be produced. Coordinate input data can be either Cartesian or fractional, originating from crystal structure determination programs such as SHELXS, refinement programs such as SHELXL or otherwise.

PLUTON may be considered as a completely redesigned and considerably expanded variety of the popular program PLUTO(78) by Motherwell and Clegg. Drawings are produced either on a display surface (graphics terminal or workstation) called DISPLAY or as a meta-file saving graphics instructions (called META) for later use such inclusion in word processors (e.g. Word) or laser printer hardcopy, suitable for publication.

PLUTON is currently available only as a build-in link into the PLATON suite of programs.

Program versions are available for various platforms including DEC-UNIX, SiliconGraphics, IBM RISC/6000, VAX/VMS (including and on IBM-PC's or compatibles under MS-DOS. Several graphics devices are supported ranging from simple tektronix 4010 terminals/emulators to X-Window graphics devices.

A drawing of a molecular structure as generated by PLUTON may be thought of in three principle aspects: the content, the style and the viewpoint. The content of the drawing requires the definition of items such as ARU's (= asymmetric residue units, vide infra) making up the list of molecules and anions to be displayed, atoms within ARU's, connections between atoms (= bonds), labels, and unit cell representation. By default, connected and possibly symmetry expanded sets of atoms constituting molecules or ions will be assembled. The style of the drawing may be like a STICK model (atoms are points and bonds are single lines joining them), a SOLID ball-and-spoke, ball-and-STRAW or ball-and-ROD model, mainly differing in the default settings of the variable radii for atoms and bonds, or a space filling model with van der Waals radii assigned to each atom (also called CPK model). The atom types may be distinguished with various patterns in the black-and-white mode or colored to differentiate between the atom types. Drawings may be made in parallel projection, perspective, or stereo-pair perspective. By default, a STICK-style drawing will be generated. The view direction may be chosen with reference to molecular features such as lines and planes defined by atoms, or with reference to the unit cell or orthogonal axial systems. The view direction may be further modified by rotations, giving flexible control of the viewpoint. By default a minimum overlap view is choosen.

All input to the program is free-format, using (sub)keywords and numerical data. The input to PLUTON is normally provided in two parts: a disk file, in general produced by a program or prepared with a text editor and containing the pertinent data on the structure at hand such as atomic coordinates, followed by interactive input of the instructions via the keyboard. In general, a small set of instructions in terms of global keywords with associated default parameter settings will suffice to produce a drawing for the set of supplied atomic coordinates. Alternatively, all input may be given on the disk file or interactively from the keyboard.

More than one data set, separated by an ENDS card may be present on the disk file. This is a convenient feature for browsing the structures retrieved from the Cambridge Structural Database. In that case, an interactively supplied END statement will not stop program execution but load the next data set (use the instruction STOP 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).

Note: PLUTON is not a finished program. It is extended and improved constantly on the basis of the needs that arise as part of our research work, including many hundreds of crystal structure determinations (organic, organometallic and inorganic) carried out as part of a national crystallographic service. New features are planned. Therefore there may be some discrepancies between the actual program and this manual. It is advised to consult the on- line manual (available with the HELP ALL feature of the program) for the most current list of instructions.

Suggestions for improvement or information on errors are welcome.

Availability: The program is available free of charge from the author for use within the academic community under the condition that it is not redistributed. A licence fee is charged to profit organizations.

2.0 - 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.

A Tektronix emulator or the X-Window menu-off mode is assumed here. X-Window based implementations support both keyboard instructions and menu driven input with ain 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 respons 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 (Fig. 1), optionally followed by a bell 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 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 ( Fig. 2) or CPK GLOBE COLOR followed by PLOT (Fig. 3).

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.

3.0 - 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 of dummy cell edges). A second, orthogonal system (A, B, C) (see J.D. Dunitz, X-Ray analysis and the Structure of Organic Molecules, Cornell University Press, p235) with coordinates (XO,YO,ZO) in Angstroms is set up internally: The unit vector A is choosen along a, B as unit vector normal to a in the ab plane, and C normal to A and B. This orthogonal system is coincident with the first system when the input axes are orthogonal. The third system is the plotting coordinate system in cm: XP across the picture from left to right, YP up the picture from bottom to top and ZP out of the paper. All these axial sets are right-handed and absolute configuration is preserved in all rotations.

As atoms are input to the program, they are stored both in the X, Y, Z and the XO, YO, ZO coordinate system. The XP, YP, ZP system is used only when plotting is actually being performed. Each atom has additional information stored for it including the atom name (the embedded element name is used by default to set various radii) and various flags such as for inclusion in the plot and labelling. This data structure is known as the atom list. Duplicate entries with the same coordinates are skipped from the input stream.

The JOIN instructions (either by default or as specified) set up a list of connections (known as bond list) between atoms. Each connection is simply a pair of atom serial numbers referring to the input atom list. Some JOIN instructions also find connections between input atoms and other atoms related to the original list by crystallographic symmetry. This may include both connections to a symmetry related part of a molecule sitting on a special position or intermolecular connections. In order to store these connections for plotting, the program appends dummy symmetry-generated atoms to the atom list and marks them with a special flag.

If the final picture is to contain several molecules, as in a packing diagram, or a complete molecule for which the input atoms represent only the symmetry-independent portion of it when a molecule lies in a crystallographically special position in the unit cell, the program will have to generate XP, YP, ZP coordinates for the atoms in each of these molecules or symmetry-related molecular fragments. This is controlled by two further lists: a list of symmetry operations pertaining to the structure, input directly using the SPGR or LATT and SYMM instructions; and a list of 'molecules and ions' (known as ARU list) to be drawn (see discussion on ARU & ASU below).

The program works as follows. Instructions (free format) are read and interpreted. Various instructions add to the list of atoms and symmetry operators. The JOIN instructions set up the connections list and may also add to the atom and ARU-lists if connections between ARU's are to be generated. Plotting parameters are then set by user instructions or left at default settings. No plotting is actually done until the PLOT instruction is read. This first sets up the XP, YP, ZP plotting list of all atoms to be plotted. The information in the ARU list and the current view matrix together tell the program how to convert X, Y, Z into XP, YP, ZP. The plotting coordinates and atom radii are scaled from Angstroms to cm. and corrected for perspective if requested. In the non-stick mode, all atoms in the plotting list are drawn, allowing for obscuring of some by others and bonds, and intersection of spheres in space-filling models and bonds in the ROD mode, except that dummy atoms are not usually drawn - they are required only so that connections between molecules are possible, and will generally be duplicated by other non-dummy atoms generated in the XP, YP, ZP list by symmetry from the original input atoms. Following the atoms, all the bonds are drawn, omitting portions obscured by atoms or bonds. Atoms are labelled by a routine which minimises overlap of the labels by atoms, bonds and other labels. When the picture is complete, the next instruction may be read.

Most data are stacked in a large array, either bottom-up or top down, so that the stack size is the limiting factor for the size of the problem that the program can handle. The program reports on the maximum memory usage in the current run. The stack size is a program implementation parameter.

The input list of atoms is checked on redundancy.

DATA and INSTRUCTION FILES

The order in which data are read is as follows:

The primary datafile (e.g. sucrose.spf) is read. When an EOF or ENDS line is encountered:
A file named sucrose.def (when present) is read.
Saved Instructions are read
Instructions from the keyboard or Mouse-clicks are processed

4.0 - Terms and Notions.

Connected sets of atoms are assembled in the following way. The procedure is started by first fixing a suitable atom. Next symmetry operations are performed on all atoms in the input set to find atoms that are connected to it. Atoms that are found to be connected are fixed as well and used to fix yet other, possibly symmetry transformed, atoms bonded to them as well. This procedure continues until no new bonded atoms are found. In the simple case of one chemical unit per asymmetric unit this constitutes an object named a molecule and is denoted with the identity code 1555. Symmetry related molecules are denoted by the general code sklm, where s is the number of the symmetry operation of the space group and k,l and m translation components. Chemical units may extend over more than one asymmetric unit. They may have a symmetry element that coincides with the space group symmetry such as an inversion centre or a screw axis. In such cases we will find atoms in the above search for a connected set of atoms that are bonded to the connected set at a position different from the one that was fixed in view of an earlier connection. Those atoms are added to the connected set and marked as symmetry related. The symmetry operation of this atom with respect to the primary one is coded and added to the molecule (aru) list. A chemical unit around an inversion centre thus consists in the PLUTO78 terminology of two molecules: 1555 and 2555. A further complication may be the presence of more than one crystallographically independent chemical unit in the unit cell (including solvent molecules and anions). In that case not all atoms will be fixed when the above procedure comes to an end when no more connected atoms are found. In that case a new residue is started by again arbitrarily fixing a suitable atom and expanding it to a connected set. A particular residue r within a molecule is indicated with the code sklm.r (e.g. 3564.03). It is understood that the code without a fraction stands for the full collection of residues. Thus in the case of two residues the molecule code 2562 is equivalent with the two residue codes 2562.01 and 2562.02. In order to be more precise two new terms have been introduced in PLUTON and PLATON. The basic structural unit is the asymmetric residue unit ( = aru ) coded as sklm.r. A molecule (ion) will will be an assembly of at least one aru. The set of aru's making up the asymmetric structural unit are called asu and encoded as sklm.

Disorder. Based on the supplied population parameters attemps are made to suppress bonds between disorder parts with unequal population parameter values.

5.0 - PLUTON INSTRUCTION SUMMARY

The order of data input and instructions is fairly flexible. However, CELL, SPGR (or LATT and SYMM) or ANGSTROM data, if any, and atomic coordinate data should preceed any PLOT or qualifier instruction. CELL and SPGR (or LATT and SYMM) must come before ATOM. The order and number of content, style and viewpoint instructions is completely flexible, except for that all desired parameter values must be set before the next PLOT instruction. An interactive graphics session will consist of a repeated cycle of qualifier and PLOT instructions. The END line is the last instruction and may be used to finish the plot session in an orderly fashion (see also STOP and QUIT).

By using the default settings associated with the choosen plot style (e.g. ROD) only a few of the available instruction types are absolutely required to produce a preliminary drawing of a structure. The absolute minimum input is a set of Angstrom coordinates, a PLOT instruction and END to stop the program.

PLUTON - MANUAL

1.0 - INTRODUCTION TO PLUTON

2.0 - INTRODUCTORY EXAMPLE

3.0 - ON HOW IT WORKS

DATA and INSTRUCTION FILES

4.0 - Terms and Notions.

5.0 - PLUTON INSTRUCTION SUMMARY

VIEW INSTRUCTIONS

6.0 - PARAMETER FILE

CARD TYPES RELEVANT TO PLUTON

THE SHELX STYLE FORMAT

ANGSTROM DATA FORMAT

APPENDIX - I : SPACE GROUP SYMMETRY