at 3.24p EDT on 2003 December 07 Sunday Miguel Howard said:
> >> > - Given that there are no hydrogens in the file ... How do
> >> > you calculate the 'angles' from the bonds that are present?
> >> Don't know that...
> > calculate the position of the hydrogen on the donor.
> OK ... how?
> > 2. if true, count up the hbond "potentials" - lone pair(s) and
> > hydrogen(s). if more than zero, add atom to table of donors and
> > acceptors.
> But, there are rarely any explicit hydrogens in .pdb files.
true - about 85% of the structures in the PDB are crystals, and I assume most
of them lack hydrogens. but we can infer the existence of a hydrogen -
rasmol does this very thing when calculating the default sphere radii to use.
(C, N, and O atoms that *should* have a hydrogen are given modified vdw radii
to account for the missing proton.)
in addition, based on the covalent bonding and group properties, we can
calculate the existence of likely lone pairs (for example, an O in a carbonyl
group will have two lone iars; an O in a hydroxyl will have one LP and an
> > 3. are there any hbond partners within correct distance (if acceptor
> > look for donors; if donor, look for acceptors)? in the majority of
> > protein and nucleic acids, the answer here will be yes - there are very
> > few hbond potentials left unsatisfied. will have to loop this to
> > account for atoms with multiple hbond potentials.
> > 4. if true, is the X-H-Y angle acceptable? I haven't thought about this
> > in depth yet but it would likely include calculating the position of the
> > involved H.
> Correct, but this may be required for the other things as well.
see my first response above ;-)
> > 5. if true, show hbond.
> > just a thought: if processing time is an issue (when isn't it?),
> Frankly, my initial answer is "No, processing time is not an issue".
> This code is executed once, at the user's request. Even if it takes one or
> two seconds that is OK. And so far I haven't seen anything which would
> lead me to believe that it should take that long.
unless some kindly list subscriber chimes in first, I will continue
investigating the process for calculating hydrogen position and get back to
you as soon as possible...
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