split pdb into submodels
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8 weeks ago
Xylanaser ▴ 80

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

pdb protein • 152 views
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Entering edit mode
8 weeks ago
Mensur Dlakic ★ 14k

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
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