Volume 1 Chapter 7 Commands in the 3D-CONSTRAIN Sub-menu
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The concept of screens, as a set of contiguous bits set on (1) or off (0) to
indicate the presence or absence of some item of information, has been
introduced in chapter 2 with respect to searches of 1D and 2D information
fields. Bit maps of this sort are calculated and stored for each CSD entry,
and are also calculated at search time for each query input to the system. A
detailed search (e.g. a text comparison, a 2D substructure search), is only
carried out if a target entry passes the screening process: all of the
query screens must be present in the screen record for that entry.
The screening step is a search heuristic which saves a considerable amount of
computing time by rejecting, at a very early stage, entries that cannot
possibly be hits.
The development of similar heuristic bit settings to cover 3D geometric
searches is currently an area of considerable research activity in chemical
information science (see e.g. P.Willett, Three-Dimenisional Chemical
Structure Handling, Research Studies Press and John Wiley, Taunton and
Chichester UK, 1991, and references therein).
In the 3D case, the problem is compounded by the very wide range of geometrical
parameters that can be used in phrasing a 3D search. For this reason, no
generalised screening mechanisms are available and screens are established to
cover the most likely geometric search terms.
In Version 5 of the CSD (October 1992) three types of 3D screens are encoded:
This list will be extended in the future by further sets of 3D screens as they
- Intramolecular distance screens (bonded and non-bonded atoms, and distances
between atoms and the centroids of aromatic rings)
- Single torsion angle screens (involving 4 contiguous and bonded atoms)
- Adjacent torsion angle screens (involving 2 single torsion angles about
contiguous bonds in the structure)
3D screens operate differently from 2D screens in that a set of screens is
determined for each SELECT command where screening is possible. This means that
more than one set of screens can be produced for a single connectivity
instruction packet. These screens are then compared consecutively with the MASK
records to determine those structures that pass the screening.
In addition the 3D screens differ from the 2D screens in that only one of the
bits in a particular type of screen needs to overlap with that in the MASK
record for that type to be considered a hit.
Finally the 3D screens use explicitly defined ranges to determine which
screening bits are set. These ranges are calculated to produce the optimum
screen-out with respect to the current contents of the database, but as the
average size of entries in the database is increasing it is possible that these
ranges may at some point in the future need to be redetermined.
Because of these differences the following conditions apply to the use of 3D
Thus the following sections provide a general guide to the types of screens
set, rather than a definitive specification of the conditions for the setting
of each bit.
- unlike the 2D screens, the 3D screens set for a connectivity instruction
packet are not displayed when the structure is defined.
- the exact definition of each bit is not given in the documentation and
their use is restricted to the processing of SELECT commands, i.e. it is not
possible to apply SCREEN or *BTEST to these screens.
20 words in the MASK record are allocated to intramolecular distance screens.
Each word relates to a different combination of atom types as follows:
1 AA - AA 2 AA - X
3 AA - S,P,Hal 4 C - C
5 C - N 6 C - O
7 Csp2 - C 8 Csp2 - N
9 Csp2 - O 10 Carom - C
11 Carom - N 12 Carom - O
13 N - N,S,P,Hal 14 N - O,S,P,Hal
15 O - O,S,P,Hal 16 Osp3 - N,O,S,P,Hal
17 Osp2 - N,O,S,P,Hal 18 Ar Ring - N,O
19 Ar Ring - S,P,Hal 20 Ar Ring - Cnonsat
There are 7 words in the MASK record that contain screens for single torsion
angles. Unlike the distance screens which use a full word for each combination
the torsion screens contain several combinations in the same word. The torsion
angles that are used for screening are as follows:
- AA = any atom
- X = any atom except C, N, O, S, P, Hal, H, D
- Hal = halogen
- Carom = aromatic carbon
- Ar Ring = centre of an aromatic ring with a minimum of 6 members
- Cnonsat = non-saturated carbon.
word 1 Z - C ~ C - Z C - C ~ C - C
C - C ~ C - N,O,X C - C ~ C - H,D
H,D - C ~ C - H,D
word 2 Z - C ~ N - Z Z - C ~ N - H,D
H,D - C ~ N - H,D
word 3 Z - C - C - Z acyclic or cyclic Z - C - C - Z cyclic
Z - C - C - Z acyclic C - C - C - C acyclic or cyclic
C - C - C - C cyclic C - C - C - C acyclic
word 4 C - C - C - O acyclic or cyclic C - C - C - O cyclic
C - C - C - O acyclic C - C - C - N acyclic or cyclic
C - C - C - N cyclic C - C - C - N acyclic
word 5 N,O - C - C - N,O Z - C - C - X
C - C - C - X Z - C - C - H,D
H,D - C - C - H,D Z - C - X - Z
word 6 Z - C - O - Z Z - C - O - C
X,N,O - C - O - C C - C - O - C
Z - C - O - H,D
word 7 Z - C - N - Z Z - C - N - C
X,N,O - C - N - C C - C - N - C
Z - C - N - H,D
All torsion angle screens use absolute values between 0 and 180deg. so that
SELECT commands for a specified angle of -10deg. to 0deg. or 0deg. to 10deg.
would use the same screens.
- Z is any element except H,D
- X is B,Si,S,P,F,Cl,Br,I
- - for the central bond means a single bond
- ~ for the central bond means a localised or delocalised double bond
- other bonds can be any type except pi-bonds (bond type 9).
All torsion angles proceed from negative to positive, e.g. from -10deg. to
+10deg. If numbers are specified in the opposite direction, e.g. from +10deg.
to -10deg. then the range will be sector of 340deg. rather than the expected
sector of 20deg.
Where one of the valence angles in a localised/delocalised double bond
is greater than 170deg. bit screen 70 will be set; if both are greater
than 170deg. then bit screen 71 is set. In both these cases no torsion
angle is calculated as the large valence angles make the result unreliable.
There are two words in the MASK record that relate to adjacent torsion screens.
"Adjacent" refers to a situation such as A-B-C-D-E where A-B-C-D is one torsion
angle and B-C-D-E is an adjacent torsion angle. Bits are then set depending on
the ranges for both angles. The first word relates to cases where both central
bonds are cyclic and the second word to those cases where one or both of the
central bonds are acyclic.
If you experience problems with 3D searches, e.g. not hitting an expected
structure, then it is possible to turn off the 3D screens in two ways:
- Distance screens only work if the atoms are in the same residue. If you use
separate atoms, for example in a pharmacophoric pattern, then screens will only
be used if the SAME-RESIDUE command is used in the connectivity instruction
packet. If explicit hydrogens are used then SAME-RESIDUE must be used to
provide screening even if the atoms are in the same defined residue.
- Several of the atom types in the distance screens go further than the
simple elemental description and include information relating to the bond
types, e.g. Osp2 for double-bonded oxygen. As a result,
better screening can be obtained if some bonding is specified, even if the
other atoms are just declared to be any atom.
- Try to avoid using multiple bond types other than single, double and
delocalised double for the central bond of a SELECTed torsion angles.
Also, if possible, use Variable Bond Type with a selection of these types
rather than the ANY bond type option.
- All angle ranges used in both types of torsion angle 3D screens are in
multiples of 5 degrees. Better screening can be obtained if you minimise the
number of 5-degree sectors covered by a range.
For example, -4.5deg. to 4.5deg. will, in absolute terms, use only one 5-degree
sector, whereas -5.5deg. to 5.5deg. would use two.
- Even if two adjacent torsion angles have the same ranges then they should
still be specified since extra screening will occur due to the adjacent torsion
- Enter the command NOSCREENS which turns off all screening activity.
This is best done within the connectivity instruction packet involved as this
will result in the screens being deactivated only for that test.
- Switch off only the 3D screening.
In the VAX implementation this can be done by commenting out, using a ! after
the $ in column one of the followingdeclaration in the
$ assign /user_mode use_3dscreens CSD3DSCR
For other implementations it is necessary to edit routine TSTLNM in the B
section of the code.
Here, when testing for 'CSD3DSCR', the line 'TSTLNM=1' should be changed to
After editing, the code must be recompiled and relinked before the change will
have any effect.