Re: [Jmol-users] Jmol model kit and docking

2010-05-28 Thread Robert Hanson
Ah, yes. I was thinking about movies as well. An interesting aspect of this is the undo/redo capability -- there are two buffers, and you can back up and "re-write" the steps in a forward motion again. It definitely is the basis for a "story-board" approach to making animations. But it will take so

Re: [Jmol-users] Jmol model kit and docking

2010-05-28 Thread Wayne Decatur
Bob, the docking and modeling abilities are great. I think with users issuing a write statement in the console at various points while doing the docking that this would allow a way to save some of the intermediates as models so ultimately an animation of the movements can be replayed forward or

[Jmol-users] Your recent additions

2010-05-28 Thread Philip Bays
Bob and all: In 1991-92, I was just getting into molecular modeling while on sabbatical at UNC Chapel Hill. While there I got to know Fred Brooks in the computer science department. He had obtained manipulator arms from one of the National Labs (used to operate from the outside of a closed en

Re: [Jmol-users] Jmol model kit and docking

2010-05-28 Thread Robert Hanson
Right, you need the signed applet. Click the link there in that example text. On Fri, May 28, 2010 at 10:00 AM, Mio_libero wrote: > When I try to load a smile string i receive this message error from Jmol > script ERROR: java.security.AccessControlException: access denied > (java.net.SocketPermi

Re: [Jmol-users] Jmol model kit and docking

2010-05-28 Thread Mio_libero
When I try to load a smile string i receive this message error from Jmol script ERROR: java.security.AccessControlException: access denied (java.net.SocketPermission cheminfo.informatics.indiana.edu:80 connect,resolve) load >> "$CC11(C)C" << What happens? Pino Il 28/05/2010 4

[Jmol-users] News flash: Jmol reads SMILES into 3D format.

2010-05-28 Thread Robert Hanson
It's been a VERY good week. First we get a working model kit for Jmol, and now SMILES to 3D: >From the application or SIGNED applet: load SMILES "CC1C(C)c...@h]coc(=O)C1" or, simply, load $CC1C(C)c...@h]coc(=O)C1 ($ indicates SMILES, like = indicates PDB) and print load("$") or Var x =