Atom Connectivity


Changing the way atoms are connected to each other

How does Olex2 ‘decide’ whether there is a bond between atoms or not? For most structures this isn’t an issue, and the connectivity displayed in Olex2 wll be as you expect it to be. But sometimes this isn’t so easy and it is good to try and understand how Olex2 works out where there should be bonds.

Each atom has a pre-defined (but customisable!) bonding radius ($r$).

So bonds are rendered for two atoms ($A$ and $B$) at distance $d$ if

$d - r_{A} - r_{B}$ < delta

Angles are not taken into account when working out these bonds.

After selecting an atom, you can do the following

  • >>info: the radii will be printed
  • >>delta: show the value of delta used for this atom
  • >>delta 0.6: update the value of delta to ‘0.6’
  • >>CONN 8: set the maximum number of bonds for this atom to ‘8’ (default: 12)

When using the CONN command, the longest bonds are excluded first. You can also set this connectivity for groups of atoms, for example:

For all metals in current structure:

  • >>conn $M 6: sets max number of bonds for all metals in this structure
  • >>conn $M 1.7 - sets bonding radius for all metals to 1.7
  • >>conn $M 1.7 6 - sets both

You can override the default bonding radii ‘globally’ by loading them from a file:

  • >>load radii bonding - you can then choose a file containing lines with the element followed by the radius for that element.

These radii will be used for the current Olex2 session and you will have to reload the file after a restart again.

You can also adjust the connectivity table by adding custom bonds

  • select two atoms, then type >>addbond
  • select bond(s) and type >>delbond to delete existing bonds.

Showing all articles with the tag connectivity-table

addbonds

A1, A2 or atoms

Adds a bond to the connectivity list for the specified atoms. This operation will also be successful if symmetry equivalent atoms are specified.

conn

n [r] atoms

Sets the maximum number of bonds for the specified atoms to n and changes the default bond radius for the given atom type to r.

>>conn 5 \$C sets the maximum number of bonds all C atoms can have to 5 >>conn 1.3 \$C changes the bonding radius for C atoms to 1.3 (the floating point is used to distinguish between n and r in this case). >>conn 5 1.3 \$C combines the two commands above

delbond

A1, A2 or Selected bond(s)

Removes selected bonds from the connectivity list. Use this command to permanently remove bonds from the display too.