Hi everyone,
I am trying to create a model of a two domain protein that oligomerizes.
I have the structure of the single domain interaction (A binding B).
Think of it as domain orientation of a dual domain protein that also
dimerizes.
I would like to fix this structure and allow the adjacent domains to
minimize around this structure based on RDC and or NOEs.
I tried to fix the domains in the interaction as seen below. I put these
lines in the same part of the refine.py that was suggested and worked for
domain orientation. The problem is that the domains don't stay fixed at the
dimer interface.
bbStr = "(name N or name C or name CA or name O or name H or name HA)"
sh2Sel = select('resid 233:339')
sh2SideChainSel = select("not " + bbStr + " and resid 233:339")
sh3Sel= select('resid 173:229')
sh3SideChainSel = select("not " + bbStr + " and resid 173:229")
sh2aSel = select('resid 1233:1339')
sh2aSideChainSel = select("not " + bbStr + " and resid 1233:1339")
sh3aSel= select('resid 1173:1229')
sh3aSideChainSel = select("not " + bbStr + " and resid 1173:1229")
fullgroupListsh3= []
fullgroupListsh2=[]
fullgroupListsh3.append( selLogic("sh2Sel and not sh2SideChainSel",vars()) )
fullgroupListsh3.append( selLogic("sh3Sel and not sh3SideChainSel",vars()) )
fullgroupListsh3.append( selLogic("sh2aSel and not sh2aSideChainSel",vars())
)
fullgroupListsh3.append( selLogic("sh3aSel and not sh3aSideChainSel",vars())
)
dyn.fix(select('resid 1233:1339 and resi 173:229'))
dyn.setGroupList( fullgroupListsh3 )
Thanks,
Andrew Severin
Iowa State University
PhD May 2009
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