Bob,
Thank you very much for looking at it so quickly.
I tried your new version and could not get the isosurface to show – I just can
not get it to visualize. With Jmol-13 RC1, using exactly the same script I get
the isosurface to show, but it does not translate the isosurface initially.
When I was making the .jmol file I translateSelected both models with the
surface attached – when I loaded the .jmol file it skipped that step. Once the
.jmol file is loaded in to RC1, I can translateSelected the models and the
structure and isosurface move appropriately.
Thank you again.
Jay
From: Robert Hanson <[email protected]<mailto:[email protected]>>
Reply-To:
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Date: Saturday, July 21, 2012 2:13 PM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [Jmol-users] trouble with isosurface with Jmol-13.0.RC1
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]<mailto:[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
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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--
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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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
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