For the angles, let me try to describe what I mean:
you have two hetero atoms, X and Y, located less than 3.4A from each other.
one of those atoms bears a hydrogen that is not present in the coordinate
file, let's not worry about which one.
each of X and Y are further covalently bonded to at least one other protein
atom, X2 and/or Y2.
The angle created by X2--X***(H)***Y or
Y2--Y***(H)***X
must be between 120-180 degrees. Anything more acute than that is likely
not a bone fide H-bond (but may be a special type of electrostatic
interaction involving pi clouds, etc)
Yes/No?
-Tom
On Tue, Nov 4, 2008 at 2:59 PM, Robert Hanson <[EMAIL PROTECTED]> wrote:
>
>
> On Tue, Nov 4, 2008 at 2:23 PM, Thomas Stout <[EMAIL PROTECTED]>wrote:
>
>> The basic premise was: if two appropriate heteroatoms are spatially
>> located within a set range of separations (1.8-3.4A)
>
>
> whatever the numbers are, that's trivial, right?
>
> connect 1.8 3.4 {xxx} {yyy}
>
> (Using Jmol script as a stand-in for real code -- not suggesting this will
> be a Jmol script in the end.)
>
>
>
>> and disposed to one another within a certain angular spread (120-180
>> degrees) relative to the atoms to which they are covalently bonded
>
>
>
> There's the more difficult analysis. Can you define that better? Relative
> to which atoms? What exactly is the angle being measured? Do you include
> only heavy atoms there, or do we need to add H atoms? Is it an average, a
> minimum, or a maximum?
>
> I understand the basic idea - that if we had the H atom, we could check to
> see if the angle X -- H -- Y was within a certain range. Jmol does that for
> assigning the main-chain hydrogen bonds already. (Jmol calculates a position
> for the NH hydrogen, does a little calculation to estimate the "bond
> energy", and from that decides whether or not to assign a hydrogen bond
> between groups.)
>
> I'm assuming here we are not only talking about peptide bond NH hydrogens
> here (they are trivial to place) -- it's the OH and other NH hydrogens that
> could be problematic.
>
> So without the H atom we do something else -- involving the other atoms to
> which X and Y are covalently bonded.... Keep talking.....
>
> Just to summarize:
>
> 1) If the hydrogens are there, it's easy. For models containing a full set
> of H atoms, we can just about do this with a Jmol script already. "Make a
> hydrogen bond whenever there is an H connected to (O, N, S) within xx
> angstroms of (O, N, S) and having X--H--Y angle between a and b" -- that's
> pretty much just a measure command tied to a connect command.
>
> 2) When H atoms are not there -- typical PDB files -- that's where the
> difficulty begins.
>
> Certainly an interesting challenge.
>
> You define it well, and I'll implement it.
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
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