split pdb into submodels

Question

[Xylanaser]

Hey is there standalone program which split pdb into parts?

I mean like one protein sequence for example into two

something like http://www.bioinformatics.org/sms2/split_fasta.html but for pdb's

cheers

Answer 1

[Mensur Dlakic]

There is a program called pdbsplitchains in this repository:

https://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