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

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*MASK

Function

*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.

Remarks

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

*ADAT
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

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

*BATC
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.

*CODE
Journal coden

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

These are listed in Appendix 4.

*YEAR
Year of publication, recorded as 19nn.

*BCLA
Basic chemical class.

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

*MATF
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

*CATF
Category flag.

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

*TOLE
Bonding tolerance

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

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

where

In most entries the value of tol is 0.40Å.

*BITS
Number of connectivity bit screens which are set.

*NW01
Number of characters in the TEXT record of the entry.

*NW02
Number of I*4 words in the CONN record of the entry.

*NW03
Number of I*4 words in the DATA record of the entry.

2. Crystal-data

*COOR
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).

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

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

*TEMP
The temperature of data collection in Kelvin units.

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

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

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

*ZPRI
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.

*NRES
The number of chemical residues

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

*INTF
The intensity measurement flag.

Flag is

*DENM
The measured crystal density reported by the author

*DENX
The calculated crystal density reported by the author

*DENC
The crystal density calculated at the CCDC

*SIGF
The average sigma C-C bond length flag.

Flag is

*SPAC
The space group symbol, in Hermann-Mauguin notation.

3. Cell-data

*ACEL
Author's unit cell parameter a (Å)

*BCEL
Author's unit cell parameter b (Å)

*CCEL
Author's unit cell parameter c (Å)

*ALPH
Author's unit cell parameter alpha (degrees)

*BETA
Author's unit cell parameter beta (degrees)

*GAMM
Author's unit cell parameter gamma (degrees)

*RCP1
Reduced unit cell parameter a (Å)

*RCP2
Reduced unit cell parameter b (Å)

*RCP3
Reduced unit cell parameter c (Å)

*RCP4
Reduced unit cell parameter alpha (degrees)

*RCP5
Reduced unit cell parameter beta (degrees)

*RCP6
Reduced unit cell parameter gamma (degrees)

*RCVO
Reduced unit cell volume (Å3)

*CVOL
Author's unit cell volume (Å3)

4. Bit-screens

BITn
The state of bit screen number n

If the state is 1 the bit screen is set.

0 the bit screen is not set.

Examples

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':

T1 *NAME 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.