Hi all,
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!"
To verify that things were working with the selections, I then tried
sela = AtomSel('(resid 19 and name SG)')
print sela.string()
print sela.indices()
print sela.simulation()
selb = AtomSel('(resid 181 and name SG)')
print selb.string()
print selb.indices()
print selb.simulation()
The selections are indeed valid, and the simulation I get out in each
case looks
identical:
<C Simulation instance at _b0ad4003_p_Simulation>
I also tried directly passing the variables sela and selb to
addDisulfideBonds,
which should skip doing AtomSel in protocol.py (I think?) and go
directly to
the if sel1.simulation() != sel2.simulation() statement. This gives
exactly the
same
error, implying that my selections are somehow being handled
differently...
Is it possible there's a bug in the addDisulfideBond procedure, or am
I trying
to run things too early on? (Or, is there something weird with
readPDB as
opposed to using genExtendedStructure?)
Since I see the same simulation in both instances, looking at
protocol.py
implies that I should not be getting this error unless there's something
different happening when protocol.py runs AtomSel than when my
test.py runs it.
Thanks in advance for any help!
Jan
------------------------------------------------------------------
Jan K. Rainey, Ph.D.
Assistant Professor
Department of Biochemistry & Molecular Biology
Dalhousie University
Halifax, NS B3H 1X5 Canada
E-mail: jan.rainey at dal.ca
Phone: (902) 494-4632
Web: http://structbio.biochem.dal.ca/jrainey/
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