From: Frieda R. <fr...@ns...> - 2007-07-28 12:45:59
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When I save the state or write the state to a script in Jmol 11.3.6, areas of cartoon that are neither helix or sheet balloon up into large tubes when the state is restored or the script is run. This does not happen if I simply open a pdb file, put it into cartoon, save the state, and restore, but it does happen in a complex script I am working on (attached). I will send the script to Bob under separate cover. Bob, when you open the script you'll see al the ugly tubes; to test it, cartoon off cartoon on the tubes will go away - now save the state, and restore. The tubes are back. Frieda /////////////////////////////////////////// Frieda Reichsman Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |
From: Bob H. <ha...@st...> - 2007-07-29 13:22:55
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thanks. I'll look into that when I get back to Northfield next week. Frieda Reichsman wrote: > When I save the state or write the state to a script in Jmol 11.3.6, > areas of cartoon that are neither helix or sheet balloon up into large > tubes when the state is restored or the script is run. > > This does not happen if I simply open a pdb file, put it into cartoon, > save the state, and restore, but it does happen in a complex script I > am working on (attached). I will send the script to Bob under separate > cover. > > Bob, when you open the script you'll see al the ugly tubes; to test it, > cartoon off > cartoon on > the tubes will go away - now save the state, and restore. > The tubes are back. > > Frieda > > > /////////////////////////////////////////// > > > Frieda Reichsman > > Molecules in Motion > > Interactive Molecular Structures > > http://www.moleculesinmotion.com > > > /////////////////////////////////////////// > > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Splunk Inc. >Still grepping through log files to find problems? Stop. >Now Search log events and configuration files using AJAX and a browser. >Download your FREE copy of Splunk now >> http://get.splunk.com/ > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >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 |
From: Bob H. <ha...@st...> - 2007-08-05 23:07:58
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this is fixed for 11.3.8 and 11.2.8. If you need a quick fix, move the STRUCTURE commands in the state .spt information up above the MODEL STATE section. Frieda Reichsman wrote: > When I save the state or write the state to a script in Jmol 11.3.6, > areas of cartoon that are neither helix or sheet balloon up into large > tubes when the state is restored or the script is run. > > This does not happen if I simply open a pdb file, put it into cartoon, > save the state, and restore, but it does happen in a complex script I > am working on (attached). I will send the script to Bob under separate > cover. > > Bob, when you open the script you'll see al the ugly tubes; to test it, > cartoon off > cartoon on > the tubes will go away - now save the state, and restore. > The tubes are back. > > Frieda > > > /////////////////////////////////////////// > > > Frieda Reichsman > > Molecules in Motion > > Interactive Molecular Structures > > http://www.moleculesinmotion.com > > > /////////////////////////////////////////// > > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Splunk Inc. >Still grepping through log files to find problems? Stop. >Now Search log events and configuration files using AJAX and a browser. >Download your FREE copy of Splunk now >> http://get.splunk.com/ > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >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 |