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

9.3 PLATON - ANALYSE Menu

 

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Chapter. 9.3  PLATON

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•  Input lines may be continued with data on the next line by placing the symbol = at the end

of the line.  

 

3.1 Instructions preceding all calculations

These instructions will be necessary only in special situations.

ROUND (ON/OFF) 

This option defines whether primary input data and derived geometrical parameter values will

be rounded based on their standard deviations or not. The default setting is ON.

Example: ROUND OFF

 

PARENTHESES (ON/OFF)

By default, the numerical part of an atomic label will be enclosed within parentheses.

Example: PARENTHESES OFF 

INCLUDE El1 El2 ...

Only the elements specified in the include list will be included in the calculations.

Example: INCLUDE C N O

EXCLUDE El1 El2 ...

The elements in the exclude list will be excluded from all calculations.

Example: EXCLUDE H

DOAC El1 El2 ....

The elements N, O, Cl, S, F and Br are treated as potential donor/acceptor atoms for hydrogen

bonding by the program. This list will be replaced by the one specified in the instruction.

Example: DOAC N O

HBOND p1 p2 p3

Default criteria for hydrogen bonds are: distance between donor and acceptor atom less than

the sum of their van der Waals radii + p1 ( = 0.5 Å); distance H to acceptor atom less than

sum of corresponding van der Waals radii + p2 (= -0.12 Å) and angle D-H...A greater than p3

(= 100 degree). The default values may be changed with the HBOND instruction.

LSPL atom_name1 atom_name2 ..

This instruction specifies the set of atoms for which a least-squares plane should be

calculated. In this way it is possible to include special planes in the following calculations that

include the generation of least-squares planes for planar parts in the structure.

RING atom_name1 atom_name2 ...

Rings in the structure up to 8 membered are found automatically. This instruction provides a

facility to include larger rings (up to 30 membered) in the calculations. The atoms should be

specified in bonded order.

FIT At11 At21 At12 At22 .....(etc)

PLATON contains a FIT routine based on quaternion rotation (A.L. Mackay, Acta Cryst.

(1984), A40, 165-166).    

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9.3 PLATON - ANALYSE Menu

 

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Chapter. 9.3  PLATON

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The general instruction to fit two molecules or residues is as above, where atoms to be fitted

are given pairwise. Note: The FIT instruction may be broken up over more than one line.

Lines that are to be continued should end with '='.  There are two modes of operation:

1.  when specified before any CALC instruction, the actual calculation  ill be done along with

the subsequent CALC GEOM or CALC INTRA  calculation. Listing of the results will be

on the .lis' file only.

 

2.  when specified after a CALC INTRA or CALC GEOM calculations will be done directly.

Listing of the results of the calculation are both on the interactive output window and in

the listing file.

A special case is the situation where the two molecules to be fitted have similar numbering of

the atoms. The automatic sorting feature of PLATON will put the atoms in the same order. In

such a case, specification of only one atom from each of the molecules will be sufficient to fit

all non-hydrogen atoms in both molecules, e.g.

FIT O11 O21

3.2 Calculations

The full range of molecular geometry calculations will be carried out automatically with a the

single keyword instruction CALC. This includes all the calculations that may be executed

alternatively with the instruction sequence CALC INTRA, CALC INTER, CALC

COORDN  and CALC METAL.

CALC INTRA ((El1 r1 El2 r2 ..)/(TOLA p1)) (NOBOND) (NOANG)

NOMOVE)_(NOSYMM)_(VERIFY)_(TOLP_t2)'>(NOTOR) (NOLSPL) (NORING) (NOTMA) (NOBPA) (NOSTD) (WLSPL)

(NOPESD) (NOMOVE) (NOSYMM) (VERIFY) (TOLP t2) 

The default instruction CALC INTRA produces a full calculation and listing of all relevant

intra-molecular geometrical parameter options using default covalent radii drawn from

internal tables. Atoms with distances less than the sum of their covalent radii plus a tolerance

(TOLA = 0.4 Å) are considered to be bonded. The default radii values may be modified with

their explicit specification (in which case TOLA is set to zero, unless specified explicitly).

Alternatively the parameter TOLA may be modified. In the automatic radii mode an

additional 0.6 Å is added to the tolerance to catch (Earth)alkali to non-metal contacts. 

The calculation and listing of bonds, bond angles, torsion angles, least-squares planes, rings,

angles between bonds and least-squares planes and thermal motion analysis may be

suppressed with the specification of the sub-keywords NOBOND, NOANG, NOTOR,

NOLSPL, NORING, NOBPA and/or NOTMA. The calculation of standard deviations may be

suppressed with NOSTD. 

     The NOMOVE sub-keyword has the effect that atoms are left at their input positions in

the course of the generation of a connected set. 

     The sub-keyword VERIFY may be used to control the inclusion of a connection in the

bond list for plotting.

         TOLP is an out-of-plane deviation parameter (by default 0.1Å) that determines the

inclusion of an atom in the process of automatic least-squares plane search.

     NOPESD , when specified, has the effect that the e.s.d. of the plane parameters is not

included in the calculation of the e.s.d. in out-of-plane deviations.

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