Tetrahedral

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Tripos Bookshelf > SLN > Specify 3D Queries > Define Basic Features

6.2.7 Tetrahedral

Calculates the coordinates for a fourth point of a tetrahedral center which has 3 points, and the center point, already defined. Represented by a single point with a line connecting it to the central point atom.

Limitations:

If all four atoms are co-planar, the tetrahedral feature is not created, and no point is generated.
When defining lone pairs for groups, such as -OH, extension points can be used. However, for groups such as -NH₃, tetrahedral point features are required for accurate lone pair definition.

SLN Format

tetrahedral[name=feature_name;attr_def;\ 
	 target=(#.###,#.###,#.###);features=f1,f2,f3,f4;\ 
	 distance=#.###;color=name_of_color;\
	 comment="comment here"]

name=--Required. Name for the tetrahedral point.
attr_def--Optional. How to evaluate the tetrahedral point.
- SLN=sln_string--Map atoms in SLN string to those in target structure.
- SLNREF=feature_name--Map atoms in SLN of specified feature to those in target structure. The fragment and referenced feature are tied to the same evaluation of the SLN in the target structure, allowing multiple matches of the SLN pattern in the target structure.

Note:

target=--Optional. Coordinates identifying the target location of the tetrahedral point, aligns tetrahedral points found in hits to the query. If not specified, the tetrahedral point 3D position is implied from the 3D coordinates in the SLN associated with the tetrahedral point. If no coordinates available, the first hit is used as the template for the alignment of subsequent hits. Note: If spatial constraints are present, this option is ignored and alignment is based on 3D requirements of the spatial constraints.
feature=--Required. Names and/or SLN atom IDs of exactly 4 features determining the tetrahedral point.
distance=--Required. Distance (Å) from the tetrahedral point to the central (1^st) atom or feature.
color=--Optional. Color to use for the feature.
comment=--Optional. Comment describing the feature (must be in quotes).

SLN Example

 
        tetrahedral[name=tet_pt;sln=AnyN(Any)(Any);\
	 features=2,1,3,4;distance=1.9

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Defining Tetrahedral Feature in SYBYL

Menubar:

UNITY > Define Query > Manage

Select FEATURE and TETRAHEDRAL as class and type, respectively.
Press Add.
or UNITY > Features > Tetrahedral

Pick center atom of tetrahedron (must be connected to 3 others and nonplanar).
Enter distance from center atom to point being calculated.
Enter a name for tetrahedral point.

Command:

DEFINE UNITY_FEATURE TETRAHEDRAL mol_area \ atom_sel distance name

mol_area--Area containing the query.
atom_sel--Center atom of tetrahedron (must be connected to 3 others and nonplanar).
distance--Distance (Å) from center atom to point being calculated.
name--Name for tetrahedral point.

Menubar:	UNITY > Define Query > Manage Select FEATURE and TETRAHEDRAL as class and type, respectively. Press Add. or UNITY > Features > Tetrahedral Pick center atom of tetrahedron (must be connected to 3 others and nonplanar). Enter distance from center atom to point being calculated. Enter a name for tetrahedral point.
Command:	`DEFINE UNITY_FEATURE TETRAHEDRAL mol_area \` `atom_sel distance name` mol_area--Area containing the query. atom_sel--Center atom of tetrahedron (must be connected to 3 others and nonplanar). distance--Distance (Å) from center atom to point being calculated. name--Name for tetrahedral point.

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