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

yyyy is the year
mm is the month
dd is the day

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

if there is no match
if there is a partial match
if there is a perfect match
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

rP, rQ are the elemental radii of atoms P, Q
d(P-Q) is the distance between atoms P and Q
tol is the bonding tolerance.

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 0 if method not known/reported 1 if method is photographic/visual 2 if method is photographic/densitometer 3 if method is diffractometer

*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

0 if not available
1 if in range 0.001-0.005Å
2 if in range 0.006-0.010Å
3 if in range 0.011-0.030Å
4 if greater than 0.030Å

*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.

Select *MASK
The 3D-CONSTRAIN sub-menu is replaced by the *MASK sub-menu.
In the dialogue area we have:
```
Select a *MASK item for definition. Select TO-3D-CONSTRAIN to leave
sub-menu.
```
Select *MATF

A red box now surrounds *MATF in the sub-menu

In the dialogue area we have:

*MATF has been selected.
Select a *MASK item for definition. Select TO-3D-CONSTRAIN to leave
sub-menu.

Select *RFAC

A red box now surrounds *RFAC in the sub-menu

In the dialogue area we have:

*RFAC has been selected.
Select a *MASK item for definition. Select TO-3D-CONSTRAIN to leave
sub-menu.

Select BITn

In the dialogue area we have:

Input ONE Bit Screen number; <RETURN> for none.

Type 34 <RETURN>

In the dialogue area we have:

BIT34 has been selected.
Select a *MASK item for definition. Select TO-3D-CONSTRAIN to leave
sub-menu.

Select TO-3D-CONSTRAIN
The *MASK sub-menu is replaced by the 3D-CONSTRAIN sub-menu.
In the summary area the new defined parameters are displayed:
```
*MATF
*RFAC
BIT34
```
These lines are displayed in green to indicate that they are DEFINE commands.
In the dialogue area we now have the "home" prompt:
```
Search for ALL crystal fragments
OVERLAP of crystal fragments permitted
Select a menu command or TO-BUILD to return to the BUILD menu.
```
The resultant commands in the instruction document are:
```
DEFINE  *MATF
DEFINE  *RFAC
DEFINE  BIT34
```

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.

Select 3D-CONSTRAIN from the BUILD menu.

Beep

The BUILD menu is replaced by the 3D-CONSTRAIN sub-menu.

There are no atoms in the fragment! EXHAUSTIVE should be unset.
Please press <RETURN> to continue.  Thank you.

Press <RETURN>
Select EXHAUSTIVE

Search for 1 crystal fragments
OVERLAP of crystal fragments permitted
Select a menu command or TO-BUILD to return to the BUILD menu.

Select *MASK
The 3D-CONSTRAIN sub-menu is replaced by the *MASK sub-menu.
In the dialogue area we have:
```
Select a *MASK item for definition. Select TO-3D-CONSTRAIN to leave
sub-menu.
```
Select *RFAC

A red box now surrounds *RFAC in the sub-menu

In the dialogue area we have:

*RFAC has been selected.
Select a *MASK item for definition. Select TO-3D-CONSTRAIN to leave
sub-menu.

Select TO-3D-CONSTRAIN
The *MASK sub-menu is replaced by the 3D-CONSTRAIN sub-menu.
In the summary area the defined parameter is displayed:
```
*RFAC
```
This line is displayed in green to indicate that it is a DEFINE command.
In the dialogue area we now have the prompt:
```
Search for 1 crystal fragments
OVERLAP of crystal fragments permitted
Select a menu command or TO-BUILD to return to the BUILD menu.
```
Select DEFINE-STRUCTURE
The BUILD menu is restored, information scrolls through the dialogue area, terminated by:
```
Total Number of Screens Set = 0
```

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 .