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Hello Andrew--
>
> 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.
>
>
> 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 )
>
let's simplify this a bit:
bbStr = "(name N or name C or name CA or name O or name H or name HA)"
sh2Sel = AtomSel('resid 233:339')
sh2SideChainStr = "not " + bbStr + " and resid 233:339"
sh3Sel= AtomSel('resid 173:229')
sh3SideChainStr = "not " + bbStr + " and resid 173:229"
sh2aSel = AtomSel('resid 1233:1339')
sh2aSideChainStr = "not " + bbStr + " and resid 1233:1339"
sh3aSel= AtomSel('resid 1173:1229')
sh3aSideChainStr = "not " + bbStr + " and resid 1173:1229"
dyn.fix('resid 1233:1339 or resi 173:229') # note the change of 'and' to 'or'
from atomSel import intersection
dyn.group(intersection(sh2Sel,"not (%s)" % sh2SideChainStr))
dyn.group(intersection(sh3Sel,"not (%s)" % sh3SideChainStr))
dyn.group(intersection(sh2aSel,"not (%s)" % sh2aSideChainStr))
dyn.group(intersection(sh3aSel,"not (%s)" % sh3aSideChainStr))
you might see how this works.
best regards--
Charles
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