From: Eric M. <em...@mi...> - 2011-07-27 22:44:48
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<html> <body> Dear Bob,<br><br> 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".<br><br> FirstGlance defines "anomalous atoms" as atoms that are <b>not (protein,dna,rna,hetero)</b>, 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".<br><br> Some cases of anomalous atoms have been fixed in remediations of the PDB. Others have not.<br><br> I am not convinced that we want to include anomalous atoms in "ligand" (seems incorrect to me) but it can be discussed.<br><br> EXAMPLES:<br><br> 3h1p has 5 atoms (protein) in Thr57 that are anomalous, I think because there are no coordinates for its alpha carbon atom.<br> <a href="http://firstglance.jmol.org/fg.htm?mol=3h1p" eudora="autourl"> http://firstglance.jmol.org/fg.htm?mol=3h1p<br><br> </a>1h3o has 2 nitrogens (protein) in C-terminal residues Thr918 that are anomalous.<br><br> 1prc has 1 nitrogen (protein) in C-terminal Ala333 that is anomalous.<br><br> <br> These are cases I happen to have noticed. There may, of course, be many others.<br><br> -Eric<br><br> At 7/25/11, Robert Hanson wrote:<br> <blockquote type=cite class=cite cite="">Right now in Jmol "ligand" is defined as "hetero and not solvent"<br> Would this be more appropriately <br><br> not (protein or dna or rna or solvent)<br><br> ?<br><br> Would there be a problem with making that change?<br><br> Bob<br><br> -- <br> Robert M. Hanson<br> Professor of Chemistry<br> St. Olaf College<br> 1520 St. Olaf Ave.<br> Northfield, MN 55057<br> <a href="http://www.stolaf.edu/people/hansonr"> http://www.stolaf.edu/people/hansonr</a><br> phone: 507-786-3107<br><br> <br> If nature does not answer first what we want,<br> it is better to take what answer we get. <br><br> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900<br> ------------------------------------------------------------------------------<br> Storage Efficiency Calculator<br> This modeling tool is based on patent-pending intellectual property that<br> has been used successfully in hundreds of IBM storage optimization engage-<br> ments, worldwide. Store less, Store more with what you own, Move data to <br> the right place. Try It Now! <a href="http://www.accelacomm.com/jaw/sfnl/114/51427378/" eudora="autourl"> http://www.accelacomm.com/jaw/sfnl/114/51427378/</a><br> _______________________________________________<br> Jmol-users mailing list<br> Jmo...@li...<br> <a href="https://lists.sourceforge.net/lists/listinfo/jmol-users" eudora="autourl"> https://lists.sourceforge.net/lists/listinfo/jmol-users</a></blockquote> <x-sigsep><p></x-sigsep> /* - - - - - - - - - - - - - - - - - - - - - - - - - - -<br> Eric Martz, Professor Emeritus, Dept Microbiology<br> U Mass, Amherst -- <a href="http://martz.molviz.org/" eudora="autourl"> http://Martz.MolviZ.Org<br><br> </a>Top Five 3D MolVis Technologies <a href="http://top5.molviz.org/" eudora="autourl"> http://Top5.MolviZ.Org<br> </a>FirstGlance, used by Nature - <a href="http://firstglance.jmol.org/" eudora="autourl"> http://firstglance.jmol.org<br> </a>3D Wiki with Scene-Authoring Tools <a href="http://proteopedia.org/" eudora="autourl"> http://Proteopedia.Org<br> </a>Biochem 3D Education Resources <a href="http://molviz.org/" eudora="autourl">http://MolviZ.org<br> </a>ConSurf - Find Conserved Patches in Proteins: <a href="http://consurf.tau.ac.il/" eudora="autourl"> http://consurf.tau.ac.il<br> </a>Atlas of Macromolecules: <a href="http://atlas.molviz.org/" eudora="autourl"> http://atlas.molviz.org<br> </a>Interactive Molecules in Public Spaces <a href="http://molecularplayground.org/" eudora="autourl"> http://MolecularPlayground.Org<br> </a>Workshops: <a href="http://workshops.molviz.org/" eudora="autourl"> http://workshops.molviz.org<br> </a>World Index of Molecular Visualization Resources: <a href="http://molvisindex.org/" eudora="autourl"> http://molvisindex.org<br> </a>Molecular Visualization EMail List (molvis-list): <a href="http://list.molviz.org/" eudora="autourl"> http://list.molviz.org<br> </a>Protein Explorer - 3D Visualization: <a href="http://proteinexplorer.org/" eudora="autourl"> http://proteinexplorer.org<br> </a>- - - - - - - - - - - - - - - - - - - - - - - - - - - */<br> </body> </html> |