I have updated FirstGlance in Jmol to version 0.98 (http://firstglance.jmol.org). All previous URL's and links will automatically utilize the new version, although clearing the cache of your browser is recommended. This new version enables you to hide portions of the structure easily. For example, an advance online publication in Nature Struct. Mol. Biol. (NSMB, http://www.nature.com/nsmb) reports 2ES4. Here, hiding all protein makes it easy to see the considerable range of ligands present. But you can also hide arbitrary subsets of chains, residues, or even atoms by clicking on them. Moieties so-hidden remain hidden in all views, until explicitly re-displayed. Thanks to Jaime Prilusky, you can now upload PDB files from your computer. The importance of looking for specific oligomers has been emphasized by adding a prominent PQS button (Probable Quaternary Structure server at EBI, provided by Kim Henrick and Janet Thornton). PQS also gives you a single copy when the asymmetric unit (published PDB file) contains more than one copy of the molecule via crystal contacts. This is the case for the above-mentioned 2ES4, as well as 2B2A, 2FIF, 2D3G, and 2F8O in the March issue of NSMB. 1R0D in the February issue is noteworthy for having eight copies. A dramatic example of a specific oligomer (from the FirstGlance Gallery) is 1K28. PQS conveniently provides links to FirstGlance for displaying the single copy or oligomer it constructs. "More Views.." now has help for evaluating model quality, and can also display the crystal unit cell, the bound box, or the coordinate axes. It also has a new link to a server that displays protein dipole moments in Jmol (provided by Clifford Felder, Joel Sussman, and Jaime Prilusky). Planned for future version 0.99 are an automated view of contacts to any designated moieties, and location of residues specified by sequence number. Planned for future version 1.00 is support for translations to Spanish and other languages. Release dates for these versions are uncertain. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://workshops.proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.proteinexplorer.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 _______________________________________________ Jmol-users mailing list Jmol-users at lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l .