Table 7 Jmol SMARTS non-primitives

+

{…}

Selection set; include only these atoms in the final atom selection

{[#6]}C=O

Select all alpha carbons

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A(.d:x-y)B

Distance from connected atoms A and B within range x–y

C(.d:1.5-1.6)C

All aliphatic carbon–carbon bonds that are between 1.5 and 1.6 Å long

+

A(.d:!x-y)B

Optional “!” indicates “not in this range”

C(.d:!1.5-1.6)C

Select all CC bonds not in the range 1.5-1.6

+

A(.a:x-y)BC

Angle A–B–C within range x–y

C(.a:115-125)CC

All CCC with angle between 115 and 125 degrees

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A(.t:x-y)BCD

Dihedral A–B–C–D within range x–y, where x and y are in the range −180 to 180

{[CH3]}(.t:50,70)CC{[CH3]} ||{[CH3]}(.t:-50,-70)CC{[CH3]}

Find gauche methyl groups and select just them

+

$R1=“xxx”;

Replacement variables

.$R1=“C=O”; $(*[$R1])

Same as $(*C=O)

D+

(SMARTS.SMARTS)

(SMARTS).(SMARTS)

component-level grouping (with definition of a component determined by/groupByModel/and/groupByMolecule/directives in Jmol)

(F.O)

Unconnected F and O in the same component

(F).(O)

F and O in different components

(*).(*)

Only select atoms if there are multiple components