On 7/13/11 1:09 AM, MUSTAFA BUGHIO wrote:
I am trying to develop multichain model using /model-multichain.py file but as my model is pentamer in nature the example given is for dimer, i dont know how to make mult-chain.ali file and what i should mention in header since my template chains are 5 A-E the given example has only 1 :A:74 :B: option, how should i change the script to run all five chain modelling together.
Modeller simply reads a range of consecutive residues from the PDB file. The alignment header tells it which residue to start reading at, and which one to stop reading at, so that you can read only part of a PDB file. So in the example you cite we ask Modeller to start reading at residue 1:A and stop at residue 74:B, so that it reads chains A and B. In your case you would probably want to tell it to start reading at the first residue in chain A and stop at the last residue in chain E.
Ben Webb, Modeller Caretaker
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