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
sptscriptfilename)
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
sptscriptfilename)
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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