On Fri, 2006-11-10 at 19:53 +0000, Tim Stevens wrote:
> > > > Is there a way of editing an existing molecule template to introduce
> > > > links between cysteines to form disulfides? I know this can be done when
> > > > first creating the new molecule but what about at a later stage?
> > >
> > > Not yet, but in the next version you can 'unlock' a molecule so that you
> > > can change the sequence elements (linking, descriptor & CCP code) and set
> > > an intra molecule link.
> >
> > This sounds great.
>
> Actually, there appears to be a little problem with this...
>
> I was getting into the coding only to find that the data model won't
> actually let me change the residues of an unlocked molecule.
>
> Now I would definitely like to change residues, as people sometimes don't
> realise the exact sequence or linking status of a molecule until after
> they have been assigning. Whether I achieve this by doing naughty things
> with the data model (and consistency checking after) or by creating a new
> molecule and swapping everything over remains to be seen, but it may take
> longer than I thought...
I have managed to form my disulfide links (by unlocking the molecule and
specifying them all as 'link:SG') but, as you predicted, once the chain
is broken I cannot seem to relink the i-1 and i+1 residues to the
cysteines again. As a short term solution is there any xml file that I
can edit to get around this?? I'm suspecting it is not that simple!
Here was the error at the prompt:
WARNING
Error in clean-up .
original error was :
Traceback (most recent call last):
File
"/usr/local/ccpnmr/ccpnmr1.0/python/ccp/api/molecule/Molecule.py", line
3003, in __init__
raise ApiError("MolResLinkEnd of %s cannot be created while molecule
has chains" % self.molResidue.molecule.name)
ApiError: MolResLinkEnd of FactorH 2-3 cannot be created while molecule
has chains
Failure to delete incorrectly created object.
Data left in an illegal state
Exception in Tkinter callback
Traceback (most recent call last):
File "/usr/lib/python2.4/lib-tk/Tkinter.py", line 1345, in __call__
return self.func(*args)
File "/usr/local/ccpnmr/ccpnmr1.0/python/memops/gui/PulldownMenu.py",
line 282, in <lambda>
command = lambda n=n: self.setSelectedIndex(n)
File "/usr/local/ccpnmr/ccpnmr1.0/python/memops/gui/PulldownMenu.py",
line 438, in setSelectedIndex
self.callback(selected_index, self.entries[selected_index])
File
"/usr/local/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/EditMoleculePopup.py", line 268, in setDescriptor
self.molResidue =
setMolResidueChemCompVar(self.molResidue,chemCompVar)
File "/usr/local/ccpnmr/ccpnmr1.0/python/ccp/util/Molecule.py", line
193, in setMolResidueChemCompVar
molResLinkEnd = molResidue.newMolResLinkEnd(linkCode=linkCode)
File
"/usr/local/ccpnmr/ccpnmr1.0/python/ccp/api/molecule/Molecule.py", line
5861, in newMolResLinkEnd
return MolResLinkEnd(self, **attrlinks)
File
"/usr/local/ccpnmr/ccpnmr1.0/python/ccp/api/molecule/Molecule.py", line
3022, in __init__
self.delete()
File
"/usr/local/ccpnmr/ccpnmr1.0/python/memops/api/Implementation.py", line
283, in delete
obj._preDelete(objsToBeDeleted, objsToBeChecked, linkCounter,
storagesToCheck)
File
"/usr/local/ccpnmr/ccpnmr1.0/python/ccp/api/molecule/Molecule.py", line
3550, in _preDelete
raise ApiError("MolResLinkEnd of %s cannot be deleted while molecule
has chains" % self.molResidue.molecule.name)
ApiError: MolResLinkEnd of FactorH 2-3 cannot be deleted while molecule
has chains
Henry
> > > Adding or removing residues, and the ability to define intra chain
> > > links will appear later.
> >
> > I'm not sure I understand the difference between an intra chain link and
> > an intra molecule link.
>
> By intra molecule I mean specifying the links when you define the
> template, within the same template. E.g. within a monomer.
>
> By intra chain I mean between different chains in the same molecular
> systems. E.g between different monomers of a dimer.
>
> T.
>
> -------------------------------------------------------------------------------
> Dr Tim Stevens Email: [log in to unmask]
> Department of Biochemistry [log in to unmask]
> University of Cambridge Phone: +44 1223 766018 (office)
> 80 Tennis Court Road +44 7816 338275 (mobile)
> Old Addenbrooke's Site +44 1223 364613 (home)
> Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
> United Kingdom http://www.pantonia.co.uk
> -------------------------------------------------------------------------------
> ------ +NH3CH(CH(CH3)OH)C(O)NHCH(CH(CH3)CH2CH3)C(O)NHCH(CH2CH2SCH3)CO2- -------
> -------------------------------------------------------------------------------
