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")
> >
> >
> >--------------------------------------------------------------------------
> >----
> >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
>
>
>
> ------------------------------------------------------------------------------
> 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/
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
