OK, that all should be fixed.
___version=13.0.RC2
new feature: isosurface MOVE [[...matrix4f...]] moves/rotates an
isosurface (for the state)
bug fix: isosurface moved by atom connection not saved correctly in state
bug fix: isosurface SET n not saved in state or JVXL file.
bug fix: isosurface SOLVENT producing artifacts --- needed minimum
resolution
bug fix: isosurface with selected set not delivering just those vertices
for within distance calc
bug fix: isosurface CONNECT in documentation but never implemented
bug fix: Gaussian reader fails for 2-digit basis orbital names such as
"12XX"
bug fix: PNGJ creation not handling same-file or same-name issues.
bug fix: SCENE writing with toggle (pause scene 2 ... pause scene 2) in
error
bug fix: SCENE min spt script needs wrapping by pathForAllFiles
bug fix: isosurface MINSET or SET not compatible with SLAB
bug fix: show $d1 where d1 is a DRAW object broken
bug fix: calculate hydrogens incorrect for proteins
See http://chemapps.stolaf.edu/jmol/Jmol-13.zip (currently uploading
slowly)
On Sat, Jul 21, 2012 at 5:37 PM, Robert Hanson <[email protected]> wrote:
> Sorry - fixed one problem and created another. See
> http://chemapps.stolaf.edu/jmol/Jmol-13.zip
>
> You need also to use frame commands BEFORE the isosurface command, not
> after. Here's my demo:
>
> load "$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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>
>
>
> --
> 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
>
>
>
--
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
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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