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

9.3 PLATON - ANALYSE Menu

 

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:: HKLTRANS hkl on :hklt.hkp

4.3 Colour Options in PLUTON

The assignment of colour to plot-items can be done at four levels

1.  global colour

2.  per atom-type

3.  per residue-type

4.  per ARU

Option 1:Instruction:

COLOR BLACK/RED/GREEN/BLUE/YELLOW/ORANGE/VIOLET/BROWN

Option 2:

Colour assignment is done by default on the basis of element-type. The default setting may be

changed with:

COLOR TYPE atom-type col (atom-type col ..)

Colour is switched on/off with

COLOR (on/off)

or implicitly with

STRAW COLOR

This option may be combined with the 'Black-and-White' Patterns:

BWC (on/off)

Option 3:

Residues (i.e. unconnected species) can be displayed  with differing colours with:

COLOR RESD

Option 4:

ARU's may be given distinguishing colours with instructions such as

ARU red 1555.01 1556.01

ARU green 1565.01

ARU-related colours are displayed with:

COLOR ARU (on/off)

or by clicking the 'col ARU' menu field. This option may be combined with the 'Black-and-

White' patterns:

BWC (on/off)

4.4 VOID & SOLV calculations.

PLATON offers two options to detect and analyse solvent accessible voids in a crystal

structure. SOLV is a faster version of VOID. VOID is useful when, in addition to the

detection of solvent areas, a packing coefficient (Kitaigorodski) is to be calculated. The

SOLV option is used as part of a SQUEEZE calculation. Some background information may

be obtained from the paper Acta Cryst (1990) A46, 194-201. The algorithm used to detect

solvent accessible areas may be summarised as follows.

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1.  The unitcell is filled with atoms of the (symmetry expanded) structural model with van der

Waals radii assigned to each atom involved.

2.  A grid search (with approximately 0.2Å grid steps) is set up to generate a list of all

gridpoints in the unitcell which are  at a minimum distance of 1.2Å from the nearest van

der Waals  surface.

3.  The list generated under 2 is used to grow lists of gridpoints (possibly supplemented with

gridpoints within 1.2 Å around 2-list points)  constituting (isolated) solvent accessible

areas.

4.  For each set of 'connected gridpoints' a number of quantities are calculated. 

•  the centre of gravity

•  the volume of the void

•  the second moment of the distribution (The centre of gravity can be seen as a first

moment). The corresponding properties of the second moment (ellipsoid) can be

calculated via the eigenvalue/ eigenvector algorithm. The shape of the ellipsoid can

be guessed from the  square-root of the eigenvalues: a sphere will give three equal

values.

5.  For each void in the structure a list of shortest distances to atoms surrounding the void is

calculated. Short contacts to potential H-bond donors/acceptors may point to solvents with

donor/acceptor properties.

As a general remark it can be stated that crystal structures do not contain solvent accessible

voids larger than in the order of 25Å

3

 However it may happen that solvent of crystallisation

leaves the lattice without disrupting the structure. This can be the case with strongly H-

bonded structures or framework structures such as zeolites. It should also be remarked that

structures have a typical packing index of in the order of 65 %. However, the missing space is

in small pockets, too small to include isolated atoms.

4.5 ASYM-VIEW 

This option may be used to get an overview over the dataset in reciprocal space in terms of

resolution, data quality and missing data. The feature requires a  name.RES or name.CIF file

and a name.HKL or name.FCF structured reflection file and is invoked via 'ASYM-VIEW' on

the opening window. Data completeness is an important issue for CCD and imageplate

derived  datasets.

A series of resolution rings is shown [sin(

θ) /λ] starting at 0.50 in steps of 0.05. The red ring

represents the 'critical' 0.6 (about 25 degrees for MoKa) minimum resolution level required

for Acta Cryst papers. Only a hemisphere of data is shown if Friedel related reflections are

averaged.

Reflections in the asymmetric section of the hemisphere are represented by 'L' for weak

reflections, '*' for those with intensities > 10 sigma(I) or the number of sigma's. Symmetry

related sections show a '+' for reflections with a symmetry related reflection in the asymmetric

section.  'Blank' areas either indicate missing reflections or systematic absences, left out on

the basis of the symmetry provided in the name.RES (or name.CIF) file.

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4.6 LEPAGE - metrical symmetry check

The metrical symmetry of a lattice may be investigated with the LEPAGE algorithm. The

input to the program may be a name.RES, name.CIF or similar file containing cell parameters

and lattice centring information. The feature may be invoked either via the 'METRICSYMM'

button on the PLATON opening window or with the keyword 'LEPAGE'

Note: This algorithm only gives the symmetry of the lattice. The actual symmetry may be

lower, depending on the content of the unit cell. When the content of the unitcell is known, it

is suggested to run the ADDSYM option, based on the MISSYM(C) algorithm by Y. Le Page.

4.7 Techniques for absorption correction in PLATON

PLATON implements a large variety of established techniques for correction  for absorption.

1.  Numerical Methods (Supposedly close to exact and based on FACE indexing)

•  ABST: Analytical following the Alcock version of "de Meulenaer & Tompa"

•  ABSG: Gaussian Integration (Modified from Coppens) 

•  ABSS: Spherical Correction

2.  Semi-empirical methods (based on additional experimental data)

•  ABSP: Psi-Scan data based correction (North et al.)

•  MULABS: Based on multiscanned reflection data (based on Blessing)

3.  Empirical Methods

•  DELABS: Modified implementation of the DIFABS algorithm (Walker & Stuart)

4.  ABSX: Comparison of calculated (i.e. Face-Indexed Alcock) and experimental psi-scans. 

 

4.8 MULABS - Blessing's method for absorption correction

MULABS implements a semi-empirical method for absorption correction using multiple

scanned reflections (i.e. multiple symmetry or azimuth equivalent reflection data) following

the excellent algorithm published by Bob Blessing, Acta Cryst (1995), A51, 33-38 (also

available in his SORTAV program).  MULABS as implemented in PLATON requires two

files:

1.  a reflection file name.HKL containing the redundant data set (SHELXL HKLF 4

FORMAT + DIRECTION COSINES)

2.  A small pertinent data/instruction file 'name.ABS

name.ABS should contain the following (free format) data:

TITL ..

CELL lambda a b c alpha beta gamma

SPGR name

MULABS mu radius tmin tmax l0max l1max

The CELL should correspond to that of the dataset, i.e. the one used to collect the set of

equivalent reflections. SPGR can be either P21/c or P2/m etc LATT & SYMM line if

necessary. mu should be in mm

-1

, radius  the equivalent radius (in mm),  tmin & tmax the

minimum and maximum crystal dimensions,  l0max & l1max,  respectively the even and odd

order limits of spherical harmonic expansion. Generally, only mu and radius are needed on

input.. An example

TITLE test

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