Sorry, might be a versioning issue there. I think I forgot to upload it.
Please try http;//chemapps.stolaf.edu/jmol/Jmol-13.zip again.
Here's what I see:
$ load $caffeine
$ isosurface vdw
$ isosurface offset {1 1 1}
$ show $isosurface1
frame 1.1;
isosurface ID "isosurface1" select ({0:4}) vanderWaals 100%;
isosurface ID "isosurface1" move [[1.0 0.0 0.0 1.0][0.0 1.0 0.0 1.0][0.0
0.0 1.0 1.0][0.0 0.0 0.0 1.0]];
isosurface ID "isosurface1" fill noMesh noDots notFrontOnly frontlit;
color isosurface opaque [xffa500];
That looks considerably different from what you have there.
On Sat, Jul 21, 2012 at 9:28 PM, Shore, Jay <[email protected]> wrote:
>
> 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]>
> Reply-To: "[email protected]" <
> [email protected]>
> Date: Saturday, July 21, 2012 5:37 PM
>
> To: "[email protected]" <[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]> 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]> 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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>> >_______________________________________________
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>>
>>
>>
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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
>
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> 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
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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
------------------------------------------------------------------------------
Live Security Virtual Conference
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
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
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