[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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