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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