1. What do I mean by "break FirstGlance"? Just that the proposed changes may break a number of existing resources (e.g. Proteopedia). For FirstGlance and Proteopedia specifically, I don't mind at all tweaking its scripts to accommodate what you decide to do, Bob. That is no problem given that I am now alerted to watch out for this change. I agree that having a better definition of "ligand" in Jmol is desirable.
2. From RasMol and Chime and early Jmol, I long ago accepted that "ligand" was "hetero and not solvent" because that's how those programs have been structured. And their structure reflected limitations in pre-remediation PDB files. Therefore in FirstGlance I speak of "ligand+" and explain how it differs from the usual concept of "ligand".
3. I think any atom that is a member of a group named one of the 20 standard amino acids or the 12 standard nucleotides should be "protein" or "nucleic" respectively. This would take care of the 3 cases of "anomalous atoms" I listed earlier, by deeming those atoms to be protein, and hence not "ligand".
4. What would be an ideal definition of ligand? Bob, you are far better qualified than me to decide. Here are my thoughts:
A. Should covalently bonded adducts (e.g. carbohydrate glycosylation of proteins) be excluded from "ligand"? Well, according to wikipedia, in inorganic chemistry, ligand refers to the binding of electron donor molecules to metal ions. Such binding has some covalent character. In biochemistry, one usually thinks of ligand binding as reversible -- but can we clearly distinguish ligand from substrate? And do we want to exclude covalently-linked moieties from "ligand"? I think I favor avoiding this problem by leaving covalently linked non-(protein,nucleic,water) within "ligand".
B. Should non-standard residues within protein and nucleic acid chains be excluded from ligand? I think yes. Easy since those are (almost always) HETATM.
There is at least one case where "protein and hetero" will fail to detect a non-standard residue: 1b07. In this case, the proposed new definition of "ligand" will still include this non-standard residue, but this situation is rare (possibly unique) so it is OK. (In 1b07, a non-standard residue is represented in the PDB file as ATOM GLY plus HETATM PYL. The PYL (phenylethane) is covalently linked to the nitrogen of a glycine, making an "amide N-substituted residue" that fools one receptor into thinking it is proline. There are 4 other PDB entries containing PYL: in 3, the PYL is a noncovalently bound true ligand; in the 4th (2vrm) PYL is covalently bound to the true ligand FAD.
C. Water is a true ligand but because of the quantity often present in PDB entries, it is convenient to separate it from "ligand".
Water should include deuterium oxide (DOD as in 3qf6 and 55 other entries; not D2O [see 3nzc]). Jmol currently does this, since "water", "hoh" and "dod" all select the same 199 atoms in the fully deuterated model 3qf6.
However, non-water "solvent" (notably sulfate ions) should, in my opinion, be included in "ligand".
So in conclusion, I agree with Bob's suggestion but with the modification that "solvent" become "water", so the new definition of "ligand" would be
not (protein,nucleic,water)
In FirstGlance, I will still have a "ligand+" toggle button, and include non-standard residues, and spacefill ligand+ by default, to alert people to unusual moieties within a model.
-Eric
At 7/27/11, Robert Hanson wrote:
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 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.
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
- --
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