Miguel wrote:
I have reproduced the problems with 1PPA. I am puzzled. I will
investigate.
a hint may be, there is no secondary structure defined
in 1ppa if I inserted
TURN 1 T1 SER 1 SER 1 The dummy structure
into 1ppa.pdb
no 'hbonds' where shown.
This was a good hint, but I did not grasp the significance when I first
read the message.
The problem is that the built-in algorithm for calculating secondary
structures is dependant upon hbond interactions.
Hmm. Are you sure? What's that about using angles instead of hydrogen bonds?
Eclipse reports only two access points to calcHydrogenBonds: via
AminoPolymer.calculateStructures() and in HSticks.setSize(). But I can't find
any use in calculateStructures() for the information returned by calcHbonds. If
that's true, and the calculation really isn't used, I'm just wondering if it was
supposed to be commented out. That would leave setSize(), which isn't ideal
either, but isn't that much of a concern. We could just use if(size > 0)
calcHbonds()....
Ah, one problem is that there are several methods:
calcHbonds()
only called by HSticks
calls Mmset.calcHydrogenBonds()
Mmset.calcHydrogenBonds()
called in Frame.freeze() when structures not present
called by calcHbonds()
calls ModelManager.calcHydrogenBonds()
ModelManager.calcHydrogenBonds()
called by Mmset.calcHydrogenBonds()
AminoPolymer.calcHydrogenBonds()
called by ModelManager.calcHydrogenBonds()
NucleicPolymer.calcHydrogenBonds()
called by ModelManager.calcHydrogenBonds()
A bit of a nettle, I think. Still, I don't think any of it is needed for
structure, is it?
So, if there were any structures in the file, then the internal hbond
calculations were not performed.
However, if there were no secondary structures defined in the input file
then the internal hbond calculations *do* get applied, causing undesired
interactions.
The problem only arises with files with no secondary structure then, right? We
know that calcHbonds() is being run unnecessarily when hbonds are turned OFF due
to restrict(). We also know that their diameters are immediately set to 0. I
don't think that's the problem. It must be that calculateStructure() is also
being run. But calculateStructure() doesn't seem to need hydrogen bonds.
I suggest just commenting out that calcHbonds() in calculateStructure() and
seeing if the problem goes away. It could be just that simple, and we could
worry about fundamentals later.
Bob
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Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
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