Jmol users who have wished Protein Explorer had a Jmol option: Take a look -- Protein Explorer now works with Jmol!
http://chemapps.stolaf.edu/pe/protexpl The following seem to be working, although with something this complex, who knows... -- support for Safari, MSIE, and Firefox -- loading of files from a local or network drive. -- viewing PDB files from remote servers. -- FirstView, QuickViews -- sequence and 3D-interactive sequence (3DSeq) -- saving the state as a "MolSlides" either locally or via the remote MolSlides server (I thought I had Opera support, but I lost it. Everything works until a certain point, then it won't follow through with any more setTimeout() calls.) Just the way it is, I guess. I give up! --Some modifications to Jmol were necessary, and some commands were added to make life on the Protein Explorer JavaScript side easier. These include: >> show info Molecule name ....... GAL4 (RESIDUES 1 - 65) COMPLEX WITH 19MER DNA Secondary Structure . PDB Data Records Brookhaven Code ..... 1D66 Number of Chains .... 4 Number of Groups .... 152 (55) Number of Atoms ..... 1652 (110) Number of Bonds ..... 1830 Number of Models ...... 1 Number of Helices ... 6 Number of Strands ... 0 Number of Turns ..... 0 >> select *; show chains D E A B >> select *; show sequence Model 1 Chain D: [C]1 [C]2 [G]3 [G]4 [A]5 [G]6 [G]7 [A]8 [C]9 [A]10 [G]11 [T]12 [C]13 [C]14 [T]15 [C]16 [C]17 [G]18 [G]19 Chain E: [C]20 [C]21 [G]22 [G]23 [A]24 [G]25 [G]26 [A]27 [C]28 [T]29 (etc.) >> set messageStyleChime Just does some slightly different reporting of atoms picked and selected, and scripts run. It was a busy week. I'll take a break from this now and let people react to it and brainstorm a bit. I look forward to this becoming a widely used resource. The hard part, of course, will be updating all the peripheral help and text. And finding a respectable home for it. (Could be St. Olaf....) Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
