renaming an holo PDB after the alo one

From: Francois Berenger
Date: 27 September 2011 01:44


Hello,

I have one bound complexe (a ligand + a protein in holo conformation).
I also have the apo structure for a very similar protein.

Is there a tool to create a new PDB, whose coordinates are
taken from the holo structure but residue names and numbers
are taken from the alo structure (by looking at the corresponding
residues in the output of a sequence alignment program)?

I thought about doing a script using clustalw for the alignment
part, but the task seems not trivial.

Thanks a lot,
Francois.

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From: David Veesler


Hi François,
Chainsaw should do the job for you if you input a clustal alignment.
Cheers
David

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From: Francois Berenger

Thanks! I'm happy I asked. I'll give a try at chainsaw.

Hope to not cut one of my fingers during the process...