Eric,
Once again, believe it or not, this is due to hand-editing state scripts.
State scripts are very special. You are not supposed to edit them. So what
you need to do, Eric, is edit out these two lines of your script:
connect;
connect;
For one thing, they to a very strange thing -- they delete all the bonds
and recreate them, twice. But why would you want to do that anyway? In any
case, because bond ordering was changed in 11.9.24, Jmol has ways to know
it is using a legacy script and handles this appropriately --- provided no
one has messed with the state script.
So what you need to do is take those two lines out.
Bob
Just take out the semicolon at the beginning of this (an all such) scripts
that you have been creating by hand.
Bob
On Sat, Apr 7, 2012 at 1:04 PM, Eric Martz <[email protected]>wrote:
> Dear Bob,
>
> This script
>
> http://www.proteopedia.org/wiki/scripts/User:Eric_Martz/Sandbox_8/Initial_sv40_scene/4.spt
>
> in Jmol 11.8.24 produces a simulated SV40 capsid as spacefilled
> "atoms", enclosed in an icosahedron made with black lines.
>
> The icosahedron fails to appear in Jmol 12.0.31 or 12.2.19.
>
> Test:
>
> 1. Copy the script and delete or comment out this
>
> if (loadedfileprev != "5d4099d9f7c44afcd4defe00c5a43765");
> load
> /*file*/"/cgi-bin/getfrozenstructure?5d4099d9f7c44afcd4defe00c5a43765";
> loadedfileprev = "5d4099d9f7c44afcd4defe00c5a43765";
> reloadfile = true;
> endif;
>
> 2. Start Jmol application. Download this PDB file (click on the blue
> .pdb link), drag and drop it into Jmol:
>
> http://www.proteopedia.org/wiki/index.php/Image:Sv40_capsid_360_atoms.pdb
>
> 3. Paste the modified script into the Jmol script console.
>
> Thanks, -Eric
>
>
>
> ------------------------------------------------------------------------------
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> Boundary is the first to Know...and Tell You.
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
------------------------------------------------------------------------------
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2
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