B Bond lengths and angles

A B card starts with B then a CCSL-word, which determines what else is on the card. There is no predetermined sequence for B cards. They drive the program BONDS.

DATA FOLLOWING ALLOWED CCSL WORDS:

SLAK
Data

No further data.
The presence of a B SLAK card indicates to BONDS that a separate output file, the .SLK file, is required. This file can then be used as part of the Crystal Data input to Least Squares programs which allow geometric slack constraints. The presence of a B SLAK card alters the meanings of some of the other B cards.

BMAX
Data

A real number, $B_{max}$ which is the maximum value for a bond in Å.

Assumptions made

The default for $B_{max}$ is 2.

BMIN
Data

A real number, $B_{min}$ which is the minimum value for a bond in Å.

Assumptions made

The default for $B_{min}$ is 0.

Note

BMAX and BMIN may also appear on an I card.

BOND
Data

A list of atom-labels or scattering-factor-labels followed, if a B SLAK card is present, by four real numbers.

The use of scattering-factor names is not because BONDS has any connection with scattering-factors, but because it enables the user to specify all of: e.g. C1, C2, C3 $\cdots$ etc by giving simply C. The first atom-label defines a source-atom . A grid of $5\times 5$ unit cells is searched for destination-atoms , symmetry equivalents of the remaining atoms in the list, whose distance from the source-atom is between $B_{min}$ and $B_{max}$.

If a B SLAK card is present, the last four items on the B BOND card must be the real numbers $b_1 \sigma_1 b_2 \sigma_2$. The maximum and minimum bonds are taken to be:

$$B_{max}=b_1+\sigma_1\qquad B_{min}=b_1-\sigma_1$$

When a bond is found it is written as an L BOND card to the .SLK file, with bond length = $b_2$ and allowed deviation = $\sigma_2$

Assumptions made

If only one label is given as data, all atoms are used as destination atoms. If there are no labels, all atoms are used as both source and destination.

BOTH
Data

Are as for B BOND. A B BOTH card will cause both bonds and interbond angles to be printed. It is not useful in the B SLAK context; to produce L ANGL cards, B ANGL cards should be used.

BERR
Data

No further data.
The ESDs in the calculated bond lengths are to be calculated and printed with the bond lengths themselves.

ANGL
Data

Three atom-labels followed, if B SLAK is present, by four or six real numbers.

If there is no B SLAK card this simply asks for the calculation of one angle subtended at the second atom, by bonds from it to the other two.

If there is a B SLAK card the labels may be atom-labels or scattering-factor-labels and they must be followed by the four real numbers $\phi_1 \sigma_1 \phi_2 \sigma_2$ and, optionally, $B_\phi$ and $\sigma_{max}$. If $B_\phi$ and $\sigma_{max}$ are present:

$$B_{max}=B_\phi+\sigma_{max}\quad\mbox{and}\quad B_{min}=B_\phi-\sigma_{max}$$

Assumptions made

If $B_\phi$ and $\sigma_{max}$ are absent, values are sought for $B_{max}$ and $B_{min}$ on B BMAX and B BMIN cards (or BMAX , BMIN items on an I card). If they are not found they default to:

$$B_{max}={1\over4}a\quad\mbox{where }a \mbox{ is the real cell side}\qquad B_{min}=0.$$

Note

The $B_{max}$ and $B_{min}$ are applied to the three labelled atoms as though they came from B BOND cards, except that in this case L ANGL cards (with angle = $\phi_2$ and $\sigma=\sigma_2$) are written to the .SLK file when the calculated bond angle $\phi$ is in the range $\phi_1-\sigma_1<\phi<\phi_1+\sigma_1$.

AERR
Data

No further data.
The ESDs in the calculated bond angles are to be calculated and printed with the bond angles.

EXAMPLES:

B BOND
B BOND Ca3
B BOTH O1 O4 O8 C6 C7 C9
B ANGL Oxy2 Oxy1 Oxy3

B SLAK
Z
Z This will look at all bonds starting from an atom whose
Z label starts C
Z (e.g. C1 C14 C6A but not Ca3),
Z and finishing at atoms whose label starts O.
B BOND C O 1.6 0.2 1.61 0.4
Z
Z This considers only atoms O6, C4, O7 and those related
Z to them by symmetry.
B ANGL O6 C4 O7 109 0.5 109 0.3

ROUTINES WHICH READ THE CARDS:

The main program BONDS reads and interprets B cards.