There is a program called pdbsplitchains in this repository:
github.com/ACRMGroup/bioptools
pdbset from the CCP4 package can do all kinds of manipulations on PDB files – including splitting by chain – but it requires a bit of scripting. For example, these several lines would extract chain B while excluding headers and water molecules.
pdbset xyzin 2f2f.pdb xyzout 2f2f_B.pdb << EOF
exclude headers
exclude WAT
select chain B
end
EOF
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