Re: [Jmol-users] "newbie" question....load from script

2008-03-25 Thread Angel Herráez
Hi, Thomas, welcome to Jmol world! I can see no reason for the problem you describe. Try these: 1.- open the Java console* and see if there is some error there (*find a coffee cup icon in the taskbar, bottom right of your screen, right-click on it, choose "Open Console") 2.- open Jmol console

Re: [Jmol-users] "newbie" question....load from script

2008-03-25 Thread Bob Hanson
Tom, welcome! Be sure to let us know if you are using the application or the applet -- sometimes it makes a difference. The zap command is not necessary -- it's always executed first as part of the load command. But it must have been excuted. Everything looks fine there. Try adding these first

[Jmol-users] "newbie" question....load from script

2008-03-25 Thread Thomas Stout
Hi All -- I am *just *getting started with JMol, so I apologize if this is blatently obvious, but I've run into a bit of strange behavior with scripting the applet. Is there something particularly "special" about the "load" command? I am calling out to a script file to load several PDB files, b

Re: [Jmol-users] TopMatch protein structure alignment and superposition web service

2008-03-25 Thread Angel Herraez
Markus, congratulations for the site This looks like a very promising tool. I look forward to having a test case where I can test your service. I have a couple of suggestions: 1.- It would be more useful to generate the display with 2 models/frames, rather than a pdb file with the 2 chains fus

[Jmol-users] TopMatch protein structure alignment and superposition web service

2008-03-25 Thread Markus Wiederstein
Dear Jmol users, We announce the release of TopMatch-web, a public web service for the alignment and superposition of protein structures and the instant visualization of structural similiarities. We believe that TopMatch is an exceptionally effective, accurate, and enjoyable program for the in