Question: How To Identify Rotamer States From A Pdb ?
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gravatar for nahsivar
6.2 years ago by
nahsivar10
Spain
nahsivar10 wrote:

Do you know of any simple code or package that simply outputs the rotameric state of a given residue based on any of the rotamer definitions ? (no rotations or optimization of best possible rotameric state for the given reside etc.,) just calculate Chi angles and print out the rotameric state based on them for all the side chains from a PDB. More like torsions.c or dangle for the main chains. Nothing fancier. Preferably command line based.

Almost all the graphic programs have a rotamer option, but all of them use some kind of rotamer library Dunbrack typically and tries to model the best possible state rather than outputting the current state.

Simply,

PDB -> Sidechain Chi angles -> Rotamer State (Dunbrack backbone independent librart definition )

I'd be happyto know if some code exists already

pdb python • 2.1k views
ADD COMMENTlink modified 6.2 years ago by Vladimir Chupakhin520 • written 6.2 years ago by nahsivar10
0
gravatar for Vladimir Chupakhin
6.2 years ago by
Toledo, Spain
Vladimir Chupakhin520 wrote:

Check the Bio.PDB module of Biopython package

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Vladimir Chupakhin520

There's something wrong with that link

ADD REPLYlink written 6.2 years ago by paulr80

yep, it's. fixed blabla-bla---- Your content is only 10 charactes long. The minimum is 15.

ADD REPLYlink written 6.2 years ago by Vladimir Chupakhin520
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