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

5 Dec 2014

      Dear Takaaki,

you have two options.

1. If you do not expect the dimer structure to change, you can use them 
as one unit, i.e.:

composition {
    component {
      template {
        pdb = dimerA.pdb
      }
    }
    component {
      template {
        pdb = dimerB.pdb
      }
    }

In principle, you would need a sequence file for each dimer, in which 
the sequences are concatenated (instead of listed separately), but if 
this is not provided, MRage will calculate the molecular weight from the 
structure, and this is probably suitably close.

Perhaps the single-sequence check is slightly too conservative, and is 
primarily meant to catch common errors with sequence files. In light of 
your example, it may be better to interpret it that there are two 
sequences in the model.

2. If you do expect some movement, you can specify assembly information. 
In this case, your composition stays as it is, and you need tho add this 
to the PHIL:

assembly
{
     component
     {
         file_name = dimerA-chain1.pdb
     }

     component
     {
         file_name = dimerA-chain2.pdb
     }
}

(and similarly for dimerB).

This tells MRage that once one component is located, the other one is 
possibly in the same relative orientation as dimerA-chain1.pdb and 
dimerA-chain2.pdb (if not, there are additional keywords to specify a 
transformation, primarily intended for homomultimers). There is also a 
"use_assembled" keyword that tells MRage to create an additional model 
of the dimer, but in this case, the monomer models are still present and 
used, and it is more efficient to run the dimer-only search as explained 
in 1.

Let me know if you need more help!

Best wishes, Gabor

On 2014-12-05 12:36, [email protected] wrote:
...
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:[email protected])
Discovery Research Dept. (Biostructure Gr.)
Chugai Pharmaceutical Co.,Ltd.
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Re: [phenixbb] how to use a dimer as a search model by MRage

Gabor Bunkoczi