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Hello Jan--
> I am trying to add disulfides to a protein in the python interpreter in
> xplor-nih 2.18 (running on mac os x 10.4). As an example, I would do:
>
> protocol.loadPDB("xx.pdb")
> protocol.addDisulfideBond('(resid 19 and name SG)','(resid 181 and
> name SG)')
>
> The error I get is "no disulfide bond between different Simulations!"
>
> Is it possible there's a bug in the addDisulfideBond procedure?
yes there's a bug. My apologies: a regression test for that function is
missing. I'll fix that.
Please try the following patch
*** python/protocol.py 2007-08-22 20:20:49 +0000
- --- python/protocol.py 2007-11-29 15:02:52 +0000
***************
*** 627,633 ****
if isinstance(sel1,str): sel1 = AtomSel(sel1)
if isinstance(sel2,str): sel2 = AtomSel(sel2)
! if sel1.simulation() != sel2.simulation():
raise Exception("no disulfide bond between different Simulations!")
xSim = getXplorSimulation(sel1.simulation())
- --- 627,633 ----
if isinstance(sel1,str): sel1 = AtomSel(sel1)
if isinstance(sel2,str): sel2 = AtomSel(sel2)
! if sel1.simulation().name() != sel2.simulation().name():
raise Exception("no disulfide bond between different Simulations!")
xSim = getXplorSimulation(sel1.simulation())
best regards--
Charles
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