It's not that I don't think the water bridges are meaningful from a
theoretical or descriptive perspective, just an empirical one. I guess if
they are there, someone has an algorithm that puts them there for modeling
purposes. But then wouldn't you want all the H atoms and not just Jmol's
calculation? Why mix and match? Is it the bonding?
Looks to me like 1lcd has heteroatom hydrogens specifically. That's very
interesting, because that's the hard part and would be pH-dependent. So if
Jmol can add to those just H on C, perhaps that would work. Then we do need
another setting. Or, better, we could detect that and not be so black and
white about this.
Can you find a case like this that involves an organic ligand? I'd like to
see if the heteroatom hydrogens are there.
In the mean time, I see there's a MET there with only 2 H on CH3.... Hmm....
Bob
On Mon, Jun 24, 2013 at 12:39 AM, Eric Martz <[email protected]>wrote:
> OK, great! Thanks, Bob!
>
> You asked to be convinced that hydrogens on the water are important.
> In 1lcd, there is a layer of water between the transcription factor
> protein and the DNA. These water bridges are clearly important in
> recognition of DNA by this protein (if we believe 1lcd).
>
> It appears to me that the water hydrogens are pointing in reasonable
> directions in most if not all cases. Here are a couple of pngj files
> (renamed .png) you can drag and drop into Jmol application to see.
> Waters are magenta.
> http://www.bioinformatics.org/molvis/jmol-tests/1lcd-water/
>
> In the "small" one I have hidden over half of the clutter so it is
> easier to see.
>
> In this case 1lcd is an NMR file with all hydrogens present so
> stripping out the non-water hydrogens and regenerating them could be
> skipped. However, there may be X-ray files that have hydrogen on
> water but incomplete hydrogen elsewhere (I have not found such a case
> yet) so I prefer to trust Jmol to do all the non-water hydrogen for
> all PDB files, just to keep things simple.
>
> Meanwhile I am stuck on another problem so I won't test your scripts
> for awhile. I have managed to get FirstGlance (my private development
> copy) so that it throws these errors:
>
> java.security.AccessControlException: access denied
> (java.net.SocketPermission www.rcsb.org:80 connect,resolve)
>
> I am trying to generate a simple demo of this to convince you there
> may be a bug that causes this -- but after several hours I have not
> yet succeeded in convincing myself much less you :-) .... more later....
>
> Eric
>
>
> At 6/23/13, you wrote:
> >Just a bad test script on my part. Here you go:
> >
> >set pdbaddhydrogens
> >load =1lcd 1 filter "!_H"
> >set appendnew false
> >delete HOH & 1.1
> >load append "" 1 filter "[HOH]"
> >
> >set appendnew true
> >load append "" 2 filter "!_H"
> >set appendnew false
> >delete HOH & 2.1
> >load append "" 2 filter "[HOH]"
> >
> >set appendnew true
> >load append "" 3 filter "!_H"
> >set appendnew false
> >delete HOH & 3.1
> >load append "" 3 filter "[HOH]"
> >
> >
> >
> >
> >
> >On Sun, Jun 23, 2013 at 11:59 PM, Robert Hanson
> ><<mailto:[email protected]>[email protected]> wrote:
> >Eric, I'm glad to see you like the idea. It's a rather interesting
> >mechanism of adding H atoms, as you have noticed. It is correct that
> >it works only if the structure has no H atoms. The idea being that
> >if a structure has H atoms, then we shouldn't mess with it EVEN if
> >pdbAddHydrogens is set. As you point out, there are convenient ways
> >around that -- removing H atoms during the load with load FILTER
> >"!_H" is a great solution to that. The way to do this allowing H on
> >water, if you really think that is meaningful (convince me!) is to
> >load the file first with no H atoms but with set pdbAddHydrogens TRUE,
> then do
> >
> >set pdbAddHydrogens TRUE
> >load =1lcd 1 filter "!_H"
> >delete HOH
> >set appendnew FALSE
> >load append "" 1 FILTER "[HOH]"
> >
> >Notice that I'm just loading one model. For all three it looks like
> >there is a bug. I can't get it to work myself.
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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