Chemical Crystallography Oxford: Distance And Angle Calculations

Chapter 19: Distance And Angle Calculations

CAMERON allows the user to calculate distances , angles and torsion angles.

DISTANCE

In order to perform a distance calculation two atoms lists must be generated. The first list is used as a 'starting atom' and the second list is for 'target atoms'. Distances will be calculated between atoms in separate lists BUT NOT within the lists themselves. The list may be generated in two ways:-

 DISTANCE N O

generates two lists - both of which can all the N and all the O atoms. In this case N-O, N-N and O-O distances will be found.

FROM

TO These subcommands allow to specify different starting and target atoms.

 DISTANCE FROM N TO O

will only calculated N-O distances. Note that the distance arguments may be either atoms or elements as required.

RANGE This sets the minimum and maximum ranges for displayed distances. The syntax is :-

 DISTANCE RANGE dmin dmax

distances are given in angstroms. If only TWO atoms are present in the atom list then the distance will be outputted irrespective of the range. However, as the full calculation will be carried out first there may be a time delay while the calculation proceeds.

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19.1: Method of Calculation

The distances output make use of the symmetry operators in order to find distances within the given range. The starting atom coordinates are NOT ALTERED but those of the target atoms are. The symmetry operators (and any suitable translations) are used to move the target atoms around. The output produced is:-

 N1_0      O2      2.323
 Operator x y z Translations 0 0 1
 N1_0      O2_4    1.114
 Operator -x y+1/2 -z Translations 0 0 -1

These show the N1 to O2 distances. The first distance relates to an O2 atom which does not currently exist. The operator and translations shown can be used with ADD to generate the atom if required. The second distance is to an atom (O2_4) which does exist. ie. if no pack number is given for the second atom it is not present in the current list.

ANGLE

TORSION

These commands are used to find angles and torsion angles between atoms that are in the current list. They are entered in sets of three (or four) as required.

Cameron Manual

Chapter 19: Distance And Angle Calculations

19.1: Method of Calculation