Karl Oberholser wrote: > Great work Bob. Several comments. When working in Quickviews and > making selections from the menus, the Busy indicator comes on, but the > change in the display or color does occur. After a couple occurrences > of this an error message is given in the message box, 'Error: > busy_count=x. Even after the error message is given selection which > are made from the menus are carried out, unless Contact Surfaces is > chosen then part way through the set up procedure a dialogue box opens > saying that PE is busy and you need to way until it is ready, but it > never achieves the ready state. Also the Hbond display does not work.
Yes, I'm working on that busy indicator. Note that you can clear it just be clicking on it. OK -- hbonds, contacts, surfaces -- I need to know what a "list" is in Chime. Bob > > Karl > > > >>> Bob Hanson <[EMAIL PROTECTED]> 6/3/2008 2:37 AM >>> > 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 necessar y, 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 & nbsp; > [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/l ists/listinfo/jmol > <https://lists.sourceforge.net/lists/listinfo/jmol>-users > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >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 > > -- 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 ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
