Jay, that's a bug. Somehow the isosurface CONNECT option got in the
documentation but was never implemented. It is a nice feature, because it
lets you toggle an isosurface on or off based on atom visibility.
Interestingly, an isosurface in one model can be connected to another
model. The effect of this is that only when both models are visible is the
isosurface visible.
I have implemented it for 12.3.RC2. See
http://chemapps.stolaf.edu/jmol/Jmol-13.zip
Thanks for the tip!
Bob
On Sat, Jul 21, 2012 at 12:05 PM, Shore, Jay <[email protected]> wrote:
>
>
> I am having trouble with isosurface in jmol-13.0.RC1 and would
> appreciate any help or suggestions.
>
> I want to load two pairs of cml and jvxl file (two molecules each with
> an ESP surface) and then save as a jmol file for later use.
>
> I have tried using load files for the two cml files and then loading the
> jvxl files and then connecting the appropriate isosurface to the cml file.
> While the first isosurface connects to the first cml, the second
> isosurface does not connect to the second cml.
>
> Below is the spt file that I use (java -Xmx1024m -jar Jmol.jar –s spt
> scriptfilename)
> set antialiasTranslucent ON;set antialiasImages ON;frank off;background
> white;color carbon black;load files
> "/Volumes/600G/gaussian_calcs/inorganic_acids/sulfuric_acid_opt_ccsd_cc_pvtz_density_3D.cml"
> "/Volumes/600G/gaussian_calcs/inorganic_acids/sulfurous_acid_opt_ccsd_cc_pvtz_density_3D.cml";
> select 1.1; isosurface ID 0
> "/Volumes/600G/gaussian_calcs/inorganic_acids/sulfuric_acid_opt_ccsd_cc_pvtz_density_3D.jvxl"
> color translucent; color isosurface "rwb";show isosurface; isosurface ID 0
> connect {1.1}; refresh;zoom 60; select 1.1;translate x -25% selected;
> refresh; select 2.1; isosurface ID 1
> "/Volumes/600G/gaussian_calcs/inorganic_acids/sulfurous_acid_opt_ccsd_cc_pvtz_density_3D.jvxl"
> color translucent; color isosurface "rwb";show isosurface; frame 2.1;
> isosurface ID 1 connect {2.1}; refresh;zoom 60; select 2.1;translate x 25%
> selected; select *; frame *; model *; refresh;
>
>
> I have also tried loading the first cml file, taking care of the first
> isosurface, then load append the second cml file and taking care of the
> second isosurface. This works great. Both isosurfaces are connected to
> their respective structures. Unfortunately, when I save this as a jmol
> file and then try to reopen it using jmol I get the following error:
>
> "script ERROR: java.io.FileNotFoundException:
> /Volumes/600G/gaussian_calcs/inorganic_acids/append (No such file or
> directory)"
>
> Below is the spt file that I use (java -Xmx1024m -jar Jmol.jar –s spt
> scriptfilename)
> set antialiasTranslucent ON;set antialiasImages ON;frank off;background
> white;color carbon black;load file
> "/Volumes/600G/gaussian_calcs/inorganic_acids/sulfuric_acid_opt_ccsd_cc_pvtz_density_3D.cml";
> select 1.1; isosurface ID 0
> "/Volumes/600G/gaussian_calcs/inorganic_acids/sulfuric_acid_opt_ccsd_cc_pvtz_density_3D.jvxl"
> color translucent; color isosurface "rwb";show isosurface; isosurface ID 0
> connect {1.1}; refresh;zoom 60; select 1.1;translate x -25% selected;
> refresh; select not *;load APPEND file
> "/Volumes/600G/gaussian_calcs/inorganic_acids/sulfurous_acid_opt_ccsd_cc_pvtz_density_3D.cml";
> select 2.1; isosurface ID 1
> "/Volumes/600G/gaussian_calcs/inorganic_acids/sulfurous_acid_opt_ccsd_cc_pvtz_density_3D.jvxl"
> color translucent; color isosurface "rwb";show isosurface; frame 2.1;
> isosurface ID 1 connect {2.1}; refresh;zoom 60; select 2.1;translate x 25%
> selected; select *; frame *; model *; refresh;
> [yishiba:local/scripts/SPTFiles] shore%
>
> any and all suggestion would be appreciated.
> Thank you.
> Jay
>
>
>
>
>
>
>
>
>
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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
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