Bijvoet centre for biomolecular research, vakgroep kristal- en structuurchemie, university of utrecht

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Newman plots may be examined sequentially or  for an individual one to be selected by

specifying the relevant central bond. 

PLOT ADP (nr) (COLOR) (VERIFY) (DISPLAY/PLOTTER/META)

A thermal motion ellipsoid plot is produced for residue number nr. The COLOR option

provides for the distinction of atom types in the plot (oxygen RED, Nitrogen BLUE and

halogens GREEN). The three plot angles xr, yr and zr to reconstruct the present orientation

are plotted in the lower right corner, upper left corner and lower left corner respectively. The

probability level of the ellipsoid surfaces is shown in the upper right corner. When no VIEW

instruction was given previously, the program will calculate a minimum overlap view.

Example: PLOT ADP 3 COLOR 

PLOT (STICK/SOLID/CPK) (MONO/STEREO) (HATCH/CONTOUR) (nr)

     (SHN/SHH/SHF/SHC) (VERIFY) (COLOR) (DISPLAY/PLOTTER/META)

Plots of the molecule in various styles are produced in a orientation that may be modified

with VIEW instructions. The STICK style provides a fast plot with labelled atoms. The

SOLID sub-keyword results in a ball-and-stick plot and the CPK sub-keyword in a

spacefilling plot. The COLOR option colours oxygen atoms RED Nitrogen atoms BLUE and

Halogen atoms GREEN. nr specifies the number of the residue to be plotted. The three plot

angles xr, yr and zr to reconstruct the present orientation are plotted in the lower right, upper

left and lower left corners respectively.

BOX (ON/OFF[ON]) (RATIO ratio[1.333])

By default the drawing will be surrounded with a rectangular box outline. This setting may be

changed with the ON and OFF sub-keywords. The three numbers shown in the bottom right,

top left and bottom left corner of the box are the rotation angles xr, yr and zr respectively.

These numbers may be used to reconstruct this particular orientation directly from the default

UNIT orientation via a VIEW XR xr YR yr ZR zr instruction. The default horizontal to

vertical size ratio of the box for a ADE plot is 4/3. A ratio of 1 produces a square box.

Example: BOX ON RATIO 1.0

VIEW (XR xr) (YR yr) (ZR zr) ...

The current orientation of the molecule for plotting may be modified with a VIEW

instruction: VIEW XR 45 YR -55 will rotate the molecule first clockwise about the horizontal

X-axis, followed by an anti-clockwise rotation by 55 degrees about the vertical Y-axis. VIEW

instructions are accumulative. The single keyword instruction VIEW will bring the molecule

back in the default orientation.

 

SET PROB (30/40/50)

The probability level for the ellipsoid surfaces is set by default to 50%.  Example: SET PROB

30  

3.4 General instructions

HELP (SPGR)

This instruction provides an on-line HELP facility. The SPGR option lists all space groups

known to 

PLATON. 

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LIST BONDS/ATOMS/SYMM/CELL/RADII

This provides for on-line inspection of BOND and ATOM tables, the current symmetry,

CELL dimensions and default radii. 

LIST IPR/PAR (ival1 (ival2))

Intermal parameter values (see Appendix VII) may be inspected with this instruction. A range

will be listed when two values are specified and the full range when none is given.

Example:LIST PAR 3 5

SET PAR p1 p2

This instruction is not meant for general use. It provides a facility to modify internal

parameter values, in particular those with no equivalent (sub)keyword. p1 is the parameter

number and p2 the new value.

SET IPR p1 p2

This instruction is not meant for general use. It provides a facility to modify internal

parameter values, in particular those with no equivalent (sub)keyword. p1 is the parameter

number and p2 the new value.

SAVE

This instruction causes the saving of subsequent instructions on a file to be executed on all

data sets, separated by ENDS cards, on the parameter file.  

END

This results in a normal end of program when the .SPF file contains only one data set,

otherwise the program restarts for the next data set on the file.

 

QUIT

This results in an immediate stop of the program, ignoring possible further datasets on the

input file.

STOP

This results in an immediate stop of the program, ignoring possible further datasets on the

input file.

4. Other options in PLATON

4.1 Cell transformation

PLATON can be used to transform CELL, SYMM and coordinate data according to a

specified transformation matrix. The general format of the transformation instruction line is:

TRMX r11 r12 r13 r21 r22 r23 r31 r32 r33 t1 t2 t3

in which 'r11 r12 r13' expresses the new a-axis in terms of the old

e.g. a' = b + c is encoded as 0 1 1

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t1 t2 t3 indicate a shift of origin after the cell transformation.

The TRMX will affect only data following it! Symmetry operations may be protected for

transformation by placing [] e.g. SPGR [C2/C]. This may be useful when the target space

group is known and the transformation doesn't seem to work otherwise (which should of

course never happen ). The transformed data may be written out as a  SHELX .RES file  by

1.  click on proper button in the PLATON opening window, or

2.  type CALC SHELX

4.2 Transformation of hkl and SHELX style direction cosines

Although it is generally better not to touch the SHELX reflection file with a transformation

matrix (to avoid chaos), since SHELX avoids that need via specification of a transformation

matrix on the HKLF line to transform reflection data as provided to the 'CELL-standard',

PLATON provides such a tool (the HKLT option).

The following example illustrates the procedure: Two files are needed

1.  the reflection file : name.HKL     (SHELX HKLF 4 - STYLE)

2.  instruction file    : name.INS

For the transformation (P21/c to P21/n : (1 0 1/0 1 0/ -1 0 0)

   

TRMX 1 0 1 0 1 0 -1 0 0

  CELL 0.71073 10.6597 9.1517 21.8466 90.0 102.25 90.0

  SPGR P21/c

  HKLF 4 1 1 0 0 0 1 0 0 0 1 

  HKLT

or

  TITL N1848A

  CELL 0.71073 22.1829 9.1517 10.6593 90.0 105.76 90.0

  SPGR P21/n

  HKLF 4 1   1 0 1 0 1 0 -1 0 0

  HKLT 

The specification of the space group is optional. This example run would produce a new file

name.HKP and a short screen output.

:: TITL  N1848A                                                               

:: CELL  22.1829    9.1517   10.6597    90.000   105.758    90.000

2082.7

:: SPGR P21/n       

Direct Cell axes and HKL Transformation Matrix

    1.0000    0.0000    1.0000

    0.0000    1.0000    0.0000

   -1.0000    0.0000    0.0000

Coordinate Transformation Matrix

    0.0000    0.0000    1.0000

    0.0000    1.0000    0.0000

   -1.0000    0.0000    1.0000

Transformation Matrix for SHELX Direction Cosines

    0.0000    0.0000    1.0000

    0.0000    1.0000    0.0000

   -0.9848    0.0000    0.4805

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