hello
just got my laptop back after it temporarily died (!) so I was playing with
the new features. I've got a few questions and a couple of tracebacks -
sorry it's quite a long message...
The quality control reports are great, but I'm not totally clear on what
some of the column headings are and what they mean:
-in problem peaks/assign errors what does it mean by 'excessive bonds' or
'multiple 1H bonds'? The assignments seem completely reasonable to me eg
43LeuHg 43LeuHa 43LeuCg says '43Hg excessive bonds'.
-what's with the red flags for peaks with large volumes? surely they are 99%
going to be things like Hba-Hbb?
-in problem resonances what is 'type prob'? also the BMRB mean for Arg Ne is
reported here as ~93 but the ref chemical shift graph has the peak for this
spread between 80-90, and all mine seem to come around 83-5. Is it just a typo?
-in problem resonances I get the idea of the 'bound resonances' column but
why do I get a flag for 19GlyHab because it is bound to 20GluN and 19GlyCa?
the peak 'binding' it to 20GluN is in a HNcocH, assignment 20H 19Hab 20N
with these linked to 5 1 4 in the ref measurement. Also is it possible to
sort these tables to bring all the red flags to the top? for most columns
this works just because you get a flag for a high number in eg SD , but this
doesn't work for bound resonances.
I tried to run network anchoring and it seemed to be going well, running
through up to iteration 4 and then seemed to finish but actually didn't seem
to ahve produced anything except:
>>> Exception in Tkinter callback
Traceback (most recent call last):
File "/usr/lib/python2.3/lib-tk/Tkinter.py", line 1345, in __call__
return self.func(*args)
File
"/home/simon/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/NetworkAnchoring.py",
line 321, in runAnchoring
nexus=nexus)
File
"/home/simon/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/NetworkAnchoring.py",
line 941, in networkAnchorAssign
dist, minDist, maxDist = distanceFunction(intensity)
File
"/home/simon/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/NetworkAnchoring.py",
line 387, in <lambda>
distanceFunction = lambda val:getNoeDistance(val, distParams)
File
"/home/simon/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/ConstraintBasic.py",
line 1302, in getNoeDistance
dist = min(refDist / (intensity ** (1/6.0)), absMax)
ValueError: negative number cannot be raised to a fractional power
can it take the absolute value of the intensity instead to avoid this?
also when I installed the new release, my project wouldn't open until I
copied across the chemComp/other/PSR.xml for a molecule I thought I had
completely deleted from my project. It doesn't appear in any of the
molecular systems or indeed anywhere obvious from the normal analysis menus,
but is still in project.xml, Molecule.xml and Nmr.xml. Looks to me like
analysis not cleaning up after itself properly. If I try to delete it from
the general editor I get
Exception in Tkinter callback
Traceback (most recent call last):
File "/usr/lib/python2.3/lib-tk/Tkinter.py", line 1345, in __call__
return self.func(*args)
File
"/home/simon/ccpnmr/ccpnmr1.0/python/memops/editor/EditObjectPopup.py", line
449, in <lambda>
lambda: self.deleteChild(table) ])
File
"/home/simon/ccpnmr/ccpnmr1.0/python/memops/editor/EditObjectPopup.py", line
844, in deleteChild
object.delete()
File "/home/simon/ccpnmr/ccpnmr1.0/python/memops/api/Implementation.py",
line 277, in delete
obj._preDelete(objsToBeDeleted, objsToBeChecked, linkCounter,
storagesToCheck)
File "/home/simon/ccpnmr/ccpnmr1.0/python/ccp/api/Molecule.py", line 5800,
in _preDelete
raise ApiError("MolResidue of %s cannot be deleted if molecule is
finalised or has chains" % self.molecule.name)
ApiError: MolResidue of PSR cannot be deleted if molecule is finalised or
has chains
but as I say it doesn't appear in a molecular system (hence no chain) and I
don't ahve any constraints in this project either. Dunno what finalised
means. There are also other molecules which I had deleted that appear in the
general editor but not in the molecular systems popup. How can I completely
kill the little buggers?
cheers,
simon
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