[phenixbb] how to use a dimer as a search model by MRage

fukamitka at chugai-pharm.co.jp fukamitka at chugai-pharm.co.jp
Fri Dec 5 04:36:51 PST 2014


Dear all,

I have a dataset, there are 4 or 5 copies of two different hetero dimers
(i.e. 4 different chains) in au, and I'd like to use the dimers as search models.

I ran phenix.MRage with a phil file below, and it searched each chains 
separately, as expected. In this case, I want to search dimerA (containing 
chain1 and 2) and dimerB (chain3 and 4) as 2 search templates, but I couldn't
find how to specify a dimer as a component.

Using dimer.pdb and dimer.seq caused an error (sequence file can't contain
multiple sequence).  How do I write an input file?

Regards,

-------------------------
composition {
  count = 5
  component {
    sequence = dimerA-chain1.seq
    stoichiometry = 1
    template {
      pdb = dimerA-chain1.pdb
    }
  }
  component {
    sequence = dimerA-chain2.seq
    stoichiometry = 1
    template {
      pdb = dimerA-chain2.pdb
    }
  }
  component {
    sequence = dimerB-chain3.seq
    stoichiometry = 1
    template {
      pdb = dimerB-chain3.pdb
    }
  }
  component {
    sequence = dimerB-chain4.seq
    stoichiometry = 1
    template {
      pdb = dimerB-chain4.pdb
    }
  }
}
-------------------------

-----
Takaaki Fukami (mailto:fukamitka at chugai-pharm.co.jp)
Discovery Research Dept. (Biostructure Gr.)
Chugai Pharmaceutical Co.,Ltd.




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