Thank you very much Bob.
I downloaded your new Jmol version, loaded the cml and jvxl files after adding
the frame commands, and then saved the .jmol file.
When I restarted jmol and loaded the .jmol file I got the following error:
script ERROR: invalid argument
----line 7 command 7 of function_setmodelstate:
isosurface id "0" >> move << 99.999195 , 0.0
",-4.5E-7,-2,1.0,0.0,-3.6E-94.5076E-7,0.0,0.99,4.99E-70.0,0.0,0.0,1.0"
===line 7 command 7 of function_setstate:
_setmodelstate
----line 326 command 11 of
/Volumes/600G/gaussian_calcs/inorganic_acids/newest|state.spt:
_setstate
----
load "/Volumes/600G/gaussian_calcs/inorganic_acids/newest"
$
Please let me know if you need anything else to trouble shoot.
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 5:37 PM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [Jmol-users] trouble with isosurface with Jmol-13.0.RC1
Sorry - fixed one problem and created another. See
http://chemapps.stolaf.edu/jmol/Jmol-13.zip
You need also to use frame commands BEFORE the isosurface command, not after.
Here's my demo:
load "$caffeine"
calculate partialcharge
isosurface mep
write caffeine.mep.jvxl
load "$morphine"
calculate partialcharge
isosurface mep
write morphine.mep.jvxl
load files "$caffeine" "$morphine"
# NEED frame 1.1 here, or else isosurfaces will be in wrong models,
cross-connected
frame 1.1
select 1.1; isosurface ID 0 "caffeine.mep.jvxl" color translucent; color
isosurface "rwb"
isosurface ID 0 connect {1.1};
select 1.1;translate x -25% selected;
# NEED frame 2.1 here
frame 2.1
select 2.1; isosurface ID 1 "morphine.mep.jvxl" color translucent; color
isosurface "rwb"
isosurface ID 1 connect {2.1};
select 2.1;translate x 25% selected;
select *; frame *;
Also, I don't recommend SHOW isosurface. You can inspect an isosurface better
with
isosurface LIST
and
show $id
But I see that there is a problem with the state, so I'm not done yet....
Bob
On Sat, Jul 21, 2012 at 4:41 PM, Shore, Jay
<[email protected]<mailto:[email protected]>> wrote:
Angel,
Thank you very much for your suggestions. I did you first suggestion and
the .jmol file loaded fine, except the isosurfaces were not translated
like when I made the .jmol file. In making the .jmol file I had used
translateSelected which worked.
I also tried your second suggestion, which gave me a similar result, the
isosurfaces were not translated, but also neither isosurface was connected
to a model.
Thank you again for your help.
Jay
On 7/21/12 1:26 PM, "Angel Herráez"
<[email protected]<mailto:[email protected]>> wrote:
>Hello Jay
>
>Two ideas:
>
>1. you should not use FILE after APPEND. There must be a single word
>after
>load. "Load files" is only needed when multiple files are loaded in one
>command.
>That is,
>load "file1.cml";
>load append "file2.cml";
>
>2. I don't think that "select 2.1" is meaninful regarding the isosurface.
>You
>can attach isosurfaces to frames/models declaring explicitly that
>association:
>
>load files "file1.cml" "file2.cml";
>isosurface id 0 model 1.1 etc.;
>isosurface id 1 model 2.1 etc.;
>
>or something ike that; see "isosurface" options in the online scripting
>doc.
>
>It could also --maybe-- be achieved using "frame 2.1" where you use
>"select
>2.1"
>(Doc says "the surface generated is associated with the currently
>displayed
>model by default")
>
>
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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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