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

9.3 PLATON - ANALYSE Menu

 

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          WLSPL  invokes mass-weighted least-squares plane calculations as opposed to unit

weighted. 

     NOSYMM limits the search for connections within the input coordinate set without the

application of translation or rotation symmetry.

Example: CALC INTRA NOLSPL NORING

CALC GEOM (SHELX/OMEGA/MOGLI/EUCLID) (VERIFY) (NOMOVE)

(EXPAND)

This instruction executes a short intra calculation, mainly producing a list of bond distances,

bond angles and torsion angles, as an alternative for the exhaustive CALC INTRA

calculations. The sub-keyword SHELX may be used to generate an ordered coordinate file

suitable for SHELX; OMEGA generates a file suitable for the tabulation of primary and

derived parameters; MOGLI results in a DGE-file suitable for the program MOGLI and

EUCLID gives a new SPF style file.

     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 EXPAND option may be useful for the generation of a file with the complete

molecule as opposed to just the unique part. 

Example: CALC GEOM EUCLID EXPAND

CALC TMA

This invokes the execution of a rigid-body thermal motion analysis and the calculation of

derived quantities. It is automatically included in a CALC INTRA calculation.  Note: No

TMA analysis is done when the residue contains too few atoms or when the R-index of the

observed and calculated Uij's is too high.

      

CALC INTER   (El1 p1 El2 p2 ..)/(TOLR p1)

Short inter-molecular contacts are listed with this instruction. By default van der Waals radii

drawn from internal tables are used in conjunction with a default tolerance (TOLR = 0.2 Å).

Hydrogen bonds are automatically found and analyzed.

CALC HBOND (p1 p2 p3)

This instruction provides a subset of the information generated with the CALC INTER

instruction and may be of use when interest is concentrated on H-bonds. 

CALC COORDN (p1/El1 r1 El2 r2 .. (NOANG) FIVE (TBA))

This instruction provides for the analysis of co-ordination spheres. Bond distances and bond

angles are calculated for atoms within the specified sphere. By default such a calculation is

done for all atoms (excluding C and H) and with radius 3.2 Å. This default may be changed

with the specification of the desired value. Alternatively a list of selected elements and their

corresponding co-ordination radii may be specified for the co-ordination geometry

calculations. Bond angles may be excluded from the listings with the NOANG sub-keyword.

A Berry pseudo rotation analysis is carried out automatically when an atom is found to be

bonded to exactly 5 atoms. Such a calculation may be enforced for the five shortest contacts

with the sub-keyword FIVE optionally followed with the value for the trans-basal-angle

(default 150 degree). 

CALC COORDN atom_name p1

The co-ordination geometry about a single atom may be examined with this instruction.

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9.3 PLATON - ANALYSE Menu

 

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Chapter. 9.3  PLATON

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Example:CALC COORDN O3 3.2

CALC METAL (p1)

Distances between metal atoms less than p1 (default 10 Å) are calculated. This option is

included in the default CALC calculations.

CALC VOID (LIST) (GRID p1) (TOLV p2)

This option may be used to check the structure for voids as possible sites for solvents. The

GRID (default value 0.4 Å) and the minimum VOID radius (1.2 + p2 Å) may be changed

(default p2 = 0.0). The LIST option gives a map on the lineprinter. Positions with a shortest

contact distance to the van der Waals surface of at least 1.2 + p2 Å are indicated with >.

Solvent accessible areas are indicated with a dot. Blank areas indicate small voids, all other

gridpoints are within the molecular van der Waals volume. Note: This option may also be

used to study cases where the unit cell contents are misplaced with respect to the symmetry

elements, since this fault will generally result in both areas with short molecular contacts and

areas with voids.

The VOID option is more compute intensive than the rest of the instructions. It is advised to

run this option in BATCH mode.

CALC DIST (eltype p1)

A distance scan is done for all vectors between the specified element and within the specified

radius. By default a scan is done for H-atoms.

Example: CALC DIST I 4.0   

DIST atom_name1 atom_name2

With this option a distance between two specified and not necessarily bonded atoms may be

calculated between atoms in the atom array. 

ANGL atom_name1 atom_name2 atom_name3

The angle between the specified and not necessarily bonded atoms is calculated.

TORS atom_name1 atom_name2 atom_name3 atom_name4

The dihedral angle involving the four specified atoms (not necessarily bonded) is calculated.

LSPL atom_name1 atom_name2 atom_name3 atom_name4 ...

The least-squares plane determined by the specified atoms is calculated.

3.3 Plots

The program provides graphics options to support the geometry analysis.  

PLOT (LSPL/PLAN/RING/RESD) (ALONG/PERP) (HPD/HPP/CAL)

Plots of the structure viewed perpendicular to or along the various least-squares planes may

be produced for inspection.

 

PLOT NEWMAN (DISPLAY/PLOTTER/META) (at1 at2)

Newman plots are produced, provided that a CALC INTRA instruction was carried out

previously in order to prepare a file with the relevant data for all Newman projections. The

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