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The first example selects all 
carbon atoms between
residue number 40 and 100:
( name ca and resid 40:100 )The next example selects all heavy side-chain atoms:
( not ( name ca or name n or name c or name o or hydrogen ) )The next example selects all atoms in Phe residues that are within 20 Å around residue 1:
( resname phe and ( residue 1 around 20.0 ) )The next example is similar to the previous one, except that all atoms of a particular Phe residue are selected once any atom of this residue is within 20 Å from residue 1:
( byresidue ( resname phe and ( residue 1 around 20.0 ) ) )Suppose that we want to get the stereochemistry as a function of residue number. The following example tags each residue by using its
carbon atom and then computes the rms deviation of
bond lengths from ideality for all atoms of the selected residue.
for $1 in id ( name ca ) loop main constraints interaction=( byresidue ( id $1 ) )=(previous) end print threshold=0.1 bonds display $RESULT end loop main