Volume 2 Chapter 3 3D-Constrain Sub-menu *LP3

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*MASK is used to define non-geometrical attributes of an entry or structure. These items will be saved in the output parameter table and may be of use in determining whether or not to use the accepted fragment in later detailed analysis. They may also be used in statistical analysis of hit entries.


When the *MASK button is selected the *MASK sub-menu is displayed (see below) and the user is prompted to select items from it. Most of these items have been discussed in detail elsewhere but, for convenience, will be summarised again here.

The attributes are divided into four groups :

1. Entry-data

Accession date ie. the date when the entry was archived to the CSD. It takes the form yyyymmdd where All entries archived before December 1971 have ADAT 19711231

Modification date ie. the date when the entry was last modified (edited). It takes the same form as *ADAT viz. yyyymmdd.

Batch number.

New entries are processed and archived to the CSD in batches of ca. 500 entries. When an update of the CSD is released users are informed of the latest batch number in the update.

Journal coden

To each journal or part-journal the CCDC assigns a numeric coden.

These are listed in Appendix 4.

Year of publication, recorded as 19nn.

Basic chemical class.

The full list of chemical classes is given in Appendix 2.

Matching flag for crystal and chemical connectivities.

Flag is

  1. if there is no match
  2. if there is a partial match
  3. if there is a perfect match
  4. if matching is impossible

Category flag.

At present all entries exported in the CSD have category flag 3, indicating that full structure determinations have been done.

Bonding tolerance

Two atoms P and Q are considered to be bonded if :

rP +rQ -tol .LE. d(P-Q) .LE. rP +rQ +tol


In most entries the value of tol is 0.40Å.

Number of connectivity bit screens which are set.

Number of characters in the TEXT record of the entry.

Number of I*4 words in the CONN record of the entry.

Number of I*4 words in the DATA record of the entry.

2. Crystal-data

The number of atoms in the entry having crystal coordinates.

These include both the atoms of the asymmetric unit (ATOM) and symmetry-related atoms bonded to the asymmetric unit (SATOM).

The space group number as defined in International Tables for Crystallography.

The crystallographic R-factor expressed as, for example, 0.056.

The temperature of data collection in Kelvin units.

In the CSD room temperature is considered to be 295K.

The maximum atomic number of the elements present in the compound.

The Z value is the number of formula units per unit cell.

The Z' value is the Z value divided by the number of general equivalent positions of the space group.

If Z'=2 the asymmetric unit contains 2 formula units.

If Z'=0.5 the asymmetric unit contains one-half formula unit.

The number of chemical residues

The "molecular" volume defined as the reported unit cell volume divided by the Z value.

The intensity measurement flag.

Flag is

The measured crystal density reported by the author

The calculated crystal density reported by the author

The crystal density calculated at the CCDC

The average sigma C-C bond length flag.

Flag is

The space group symbol, in Hermann-Mauguin notation.

3. Cell-data

Author's unit cell parameter a (Å)

Author's unit cell parameter b (Å)

Author's unit cell parameter c (Å)

Author's unit cell parameter alpha (degrees)

Author's unit cell parameter beta (degrees)

Author's unit cell parameter gamma (degrees)

Reduced unit cell parameter a (Å)

Reduced unit cell parameter b (Å)

Reduced unit cell parameter c (Å)

Reduced unit cell parameter alpha (degrees)

Reduced unit cell parameter beta (degrees)

Reduced unit cell parameter gamma (degrees)

Reduced unit cell volume (Å3)

Author's unit cell volume (Å3)

4. Bit-screens

The state of bit screen number n

If the state is 1 the bit screen is set.

0 the bit screen is not set.


Ex.1 This example illustrates a typical dialogue, having already built a search fragment.

Note that, at any time while you are in the *MASK sub-menu, a selected *MASK item can be de-selected by simply reselecting it. The red box around the item will then vanish.

Once you have returned to the 3D-CONSTRAIN sub-menu you can only deselect an item by using the DEL-INSTRUCTIONS command.

Ex.2 This example illustrates a dialogue when no search fragment has been built.

Suppose a test has been constructed to search compound names for the string `penicill':


Suppose you wish to tabulate the R-factor for each kept hit.

Note: It is essential to complete the above dialogue with the selection of DEFINE-STRUCTURE in the 3D-CONSTRAIN sub-menu so that a pseudo-3D test is defined.

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Volume 2 Chapter 3 3D-Constrain Sub-menu PARAMETER.