Yes, we did notice the nonprotein N-terminus atoms. Actually, I think those
should be included explicitly in "protein" -- Is there some reason not to do
that?
Well, hmm. When you say "break First Glance" what do you mean Eric? Why
wouldn't you just adapt it to this slightly different definition? So you are
saying that First Glance uses the "ligand" term specifically for
hetero and not solvent
?
Isn't that definition pretty much useless? Why would that be useful? The
"hetero" designation is basically useless. It could be anything, of course,
including protein that is not "atom" based. As you point out:
*Anomalous Atoms*: *?* (Controlled by the Labels
Checkboxes<http://molvis.sdsc.edu/fgij/notes.htm?mol=3H1P#labels>and
under
*More Views..*)
Anomalous atoms were a problem in version 1.0 of *FirstGlance*. Since
version 1.0 was released in 2007, improvements in Jmol, and remediations of
the PDB have largely eliminated the problem of anomalous atoms.
*Definition.* Atoms that are not recognized by Jmol as being one of:
protein, nucleic acid, or "hetero".
*Rationale:* According to the rules for PDB files, all atoms that are not
members of standard residues in protein or nucleic acid chains should be
designated "hetero". Hetero atoms are typically further subdivided: there is
"solvent" (water and some inorganic anions such as sulfate and phosphate),
and everything else is "ligand". Rare PDB files don't follow the rules, and
these confuse Jmol. And rarely, Jmol may interpret PDB files incorrectly.
The result is atoms that are *neither protein, nucleic acid, nor hetero*.
Within *FirstGlance*, these are deemed *anomalous atoms*. *Problem.* *
FirstGlance* will often fail to display anomalous atoms appropriately. Some
anomalous atoms could be invisible in all views except Vines (with details
on).
*Solution.* In order to avoid leaving anomalous atoms invisible, they are
initially always shown as dot surfaces of van der Waals radii (see snapshot
at right), and labeled *?*. These labels can be hidden, brought to the
front, or expanded into full identifications with the Labels
Checkboxes<http://molvis.sdsc.edu/fgij/notes.htm?mol=3H1P#labels>.
Eric, how hard would it be for you to just search for "ligand" in your
scripts and just change those to "(hetero and not solvent)"? That should be
easy enough, right?
We're trying to get a truly useful definition of "ligand" and it just is not
"hetero and not solvent" since "hetero" can certainly include protein. Take,
for example:
load =1e6y
print {hetero and protein}.group.count()
AGM
24
GL3
8
MHS
22
OCS
18
SMC
14
TP7
42
Maybe one wants to check on the hetero groups, and maybe one wants to
exclude water, but "ligand" is just totally inappropriate.
On Wed, Jul 27, 2011 at 5:43 PM, Eric Martz <[email protected]>wrote:
> Dear Bob,
>
> This change would give different results in a few cases, and would break
> the existing code in FirstGlance in Jmol. The new definition would include
> what have been "ligand" atoms, plus what I call "anomalous atoms".
>
> FirstGlance defines "anomalous atoms" as atoms that are *not
> (protein,dna,rna,hetero)*, namely, atoms that Jmol fails to assign to one
> of these categories. Every atom should, in principle, be assigned to one of
> these 4 categories, in an ideal world, I believe. FirstGlance shows
> anomalous atoms, by default, spacefilled, as dot surfaces, and marked with
> "?", as a caution. In fact, it also includes them in its category "ligands+"
> to be "better safe (and see them) than sorry". Controls for display of
> anomalous atoms are under "More Views".
>
> Some cases of anomalous atoms have been fixed in remediations of the PDB.
> Others have not.
>
> I am not convinced that we want to include anomalous atoms in "ligand"
> (seems incorrect to me) but it can be discussed.
>
> EXAMPLES:
>
> 3h1p has 5 atoms (protein) in Thr57 that are anomalous, I think because
> there are no coordinates for its alpha carbon atom.
> http://firstglance.jmol.org/fg.htm?mol=3h1p
>
> 1h3o has 2 nitrogens (protein) in C-terminal residues Thr918 that are
> anomalous.
>
> 1prc has 1 nitrogen (protein) in C-terminal Ala333 that is anomalous.
>
>
> These are cases I happen to have noticed. There may, of course, be many
> others.
>
> -Eric
>
>
> At 7/25/11, Robert Hanson wrote:
>
> Right now in Jmol "ligand" is defined as "hetero and not solvent"
> Would this be more appropriately
>
> not (protein or dna or rna or solvent)
>
> ?
>
> Would there be a problem with making that change?
>
> Bob
>
> --
> 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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--
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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