Good point, Eric.... Which reminds me that my local implementation also
requires a "ligand" to have >5 covalently bonded atoms, this is meant to
screen out anomolous/spurious single atoms/ions and also uninteresting (to
me) things like imidazole. But, I am specifically interested in synthetic,
inhibitor molecules as ligands. The "meaning" of ligand is much broader
than just that....
-Tom
On Wed, Jul 27, 2011 at 3:43 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
>
> ------------------------------------------------------------------------------
> Storage Efficiency Calculator
> This modeling tool is based on patent-pending intellectual property that
> has been used successfully in hundreds of IBM storage optimization engage-
> ments, worldwide. Store less, Store more with what you own, Move data to
> the right place. Try It Now!
> http://www.accelacomm.com/jaw/sfnl/114/51427378/
>
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> **
>
> ** /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Eric Martz, Professor Emeritus, Dept Microbiology
> U Mass, Amherst -- http://Martz.MolviZ.Org
>
> <http://martz.molviz.org/>Top Five 3D MolVis Technologies
> http://Top5.MolviZ.Org
> <http://top5.molviz.org/>FirstGlance, used by Nature -
> http://firstglance.jmol.org
> 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org
> <http://proteopedia.org/>Biochem 3D Education Resources http://MolviZ.org
> <http://molviz.org/>ConSurf - Find Conserved Patches in Proteins:
> http://consurf.tau.ac.il
> Atlas of Macromolecules: http://atlas.molviz.org
> Interactive Molecules in Public Spaces http://MolecularPlayground.Org
> <http://molecularplayground.org/>Workshops: http://workshops.molviz.org
> World Index of Molecular Visualization Resources: http://molvisindex.org
> Molecular Visualization EMail List (molvis-list): http://list.molviz.org
> Protein Explorer - 3D Visualization: http://proteinexplorer.org
> - - - - - - - - - - - - - - - - - - - - - - - - - - - */
>
>
> ------------------------------------------------------------------------------
> Got Input? Slashdot Needs You.
> Take our quick survey online. Come on, we don't ask for help often.
> Plus, you'll get a chance to win $100 to spend on ThinkGeek.
> http://p.sf.net/sfu/slashdot-survey
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
------------------------------------------------------------------------------
Got Input? Slashdot Needs You.
Take our quick survey online. Come on, we don't ask for help often.
Plus, you'll get a chance to win $100 to spend on ThinkGeek.
http://p.sf.net/sfu/slashdot-survey
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
