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

9.3 PLATON - ANALYSE Menu

 

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H-Atoms     - In/Exclude H-Atoms toggle

PLUTON-ELD  - Direct path to PLUTON with the same connectivity.  

Probability - Displacement ellipsoid probabilities from 10 to 90 % in 

              steps of 10%. The default is 50%.

StyleB      - (not implemented)

Hetero El.s - Hetero atom octants shaded (3D ellipsoids).

Envelope El - 2-D ellipsoids

Octant El.s - Octant 3-D ellipsoids for all atoms.

ViewOptions - Starting default orientations 

              a) All angles zero

Auto-Plot   - Some option changes result in a redrawing of the image.

              This can be overrules by clicking this feature OFF.

Label -Hat+ - Global label on/off toggle. Left position for non-hydrogen

              atoms only. Right click position includes H-atom labels,

MoveLabel   - When active, atom labels may be moved to a new position.

              Clicking on the lowerleft corner of a label will delete

              it to appear again at the clickposition of a second click. 

LabelSize   - The labelsize can be changed as a function of the

              click position.

DeleteLabel - Individual labels can be deleted by clicking on them.

IncludLabel - Deleted labels (shown in red) can be reinstated by

              clicking on them.

Resd012..   - By default, all residues are drawn. This corresponds to

              the leftmost click position. The other click positions 

              bring up individual residues.

CRotY       - Continuous rotation with speed corresponding to click

              position. 

<<-RotZ+>>  - Stepwise rotation about Z (perpendicular to image).

              Stepsize and direction based on click position. 

<<-RotY+>>  - Stepwise rotation about Y (vertical in image)

              Stepsize and direction based on click position. 

<<-RotX+>>  - Stepwise rotation about X (horizontal in image)

              Stepsize and direction based on click position. 

Color       - Colour on/off toggle. 

Decoration  - Include/Exclude Border text.

EPS         - A copy of the current display (excluding menu's) is

              written in EPS (PostScript) code to a file with 

              extension '.ps' 

MenuOff End - Switch to Keyboard input (from Input Window) or

              terminate ORTEP menu. 

              To start the menu feature again type 'MENU ON'

Remarks:

•  The three numbers in the corners indicate the angles required to reconstruct the current

orientation from the default the default  orientation with a 'VIEW UNIT XROT xr YROT

yr ZROT zr' instruction.

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9.3 PLATON - ANALYSE Menu

 

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•  The image can be refreshed by either hitting or clicking on the   menu header

PLATON/ORTEP SUB-MENU

ToOptions   - Back to main PLATON/ORTEP menu

DisplayText - Display additional text toggle.

NewText     - Input on new text to move to its proper place subsequently.

MoveText    - Move Text item to new position

Textsize    - Change default textsize.

DeleteText  - Delete textitem by clicking on it.

ChTextSize  - Change size of a text item.

ViewInvert  - Invert to opposite absolute configuration.

4.18 PLATON and CSD-FDAT files

PLATON can be run on multiple entry FDAT files. An END instruction loads the next entry

from the FDAT file. Certain instructions can be saved in order to run them also for the next

entries. This can be done by activating the 'SAVE-InstrS' button. An instruction sequence is

terminated by clicking on END (or by typing END). e.g. in order to examine a set of entries:

Click 'SAVE-InstrS'

Click 'ORTEP/ADP'

Click 'END'

Click 'END'

5.  Terms and notions

5.1 The n.ijk symmetry operation on input

Atomic coordinates as input will be transformed in general by symmetry operations following

certain rules. In the default automatic mode this will result in a connected set with residues

properly positioned within the unit cell range. The symmetry operation applied to the input

data will be listed under the header trans in the atomic coordinates listing and is encoded as

n.ijk. n stands for the number of the symmetry operation as specified on the first page of the

output listing and ijk for the unit cell translations in the three directions relative to 555:

ijk=564 means 1 positive translation in the b direction, 1 negative translation in the c

direction and none in the a direction.

 

The automatic mode transformation may be overruled for a given atom by preceding the data

for that particular atom by a TRNS instruction e.g. TRNS 3.564. This facility may be used to

determine the part of the molecule that is to be considered as the asymmetric part of a

symmetrical molecule. The transformation to be applied only to the first atom as a starting

point of a new residue can be forced with a negative symmetry transformation code e.g.

TRNS -5.354. Its position in the input stream determines the atoms to which it will apply. The

input stream may contain several of such instructions, each apply to the atoms that follow

until overruled by a new one. Their effect will only be on atoms that are chosen to start a new

residue.

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5.2 Disorder

The program attempts to manage the problems that are encountered with several types of

disorder. Only two-fold disorder is allowed. Populations higher than 0.5 are understood as

major disorder components and those less than 0.5 as minor disorder components. The usual

transformations on input coordinates are restricted. In general it will be necessary to supply

disordered molecules as connected sets. The calculation of distances and angles etc. will

extend only to entities involving the major disorder component or the minor disorder

component but not both.

5.3 Molecules and Residues

The concepts of molecules and residues are related but not always synonymous within the

PLATON realm. A residue is defined as a part of the structure that is connected by intra-

molecular bonds only and is associated with a number. A structure may thus contain one or

more residues. Residues may be chemically equivalent or chemically distinct. A molecule is

defined as an asymmetric part of the structure connected by intra-molecular bonds only.

Several molecules may join by crystallographic symmetry into one residue. A particular

molecule is designated by a code: [nijk.rr] where n denotes the symmetry operation with

respect to the basic molecule, ijk the translation with respect to 555 and rr the residue number.

The structure of sucrose thus consists of two molecules (e.g. [1555.01] and [2545.01]) but

only one residue.

 

6. Parameter files

The atomic parameters (including unit cell parameters, coordinates and temperature

parameters) for a given structure may be input in various ways:  the STANDARD

PARAMETER FILE Format (SPF), SHELX  type .INS/.RES files,  simple  XYZ Angstrom

coordinate format, CIF, PDB, CSD-FDAT formats

The SPF-format is card image oriented. The first four characters on a card specify the nature

of the data that follow on that card. Data that are not needed for the current program are

simply skipped. All data are in free format.

6.1 The SPF format

TITL text

This text may be used for various titling purposes. It may be overridden at any time by

another TITL instruction.

CELL (wavelength) a b c alpha beta gamma

 Optional wavelength and cell parameters in Å’s and degrees respectively. No CELL card is

needed for Å data input. The wavelength is used for the calculation of the linear absorption

coefficient.

CESD sig(a) sig(b) sig(c) sig(alpha) sig(beta) sig(gamma)

This optional card specifies standard deviations in the cell parameters. No CESD card is

needed for Angstrom data. The cell e.s.d. is combined with the coordinate e.s.d. for the

calculation of the e.s.d. in derived parameters.

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