Examples

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Examples

The first example selects all $C^{\alpha}$ 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 $C^{\alpha}$ 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

Xplor-NIH 2025-03-21