should I be using
translate x 25% selected
or
translateSelected x 25%
I do not see "translate x 25% selected" in the manual, but in my spt script it
works well, though I am not sure that it is being interpretted when reading the
state file.
"translateSelected x 25%" does not work well in my spt file. If I:
select 1.1
translateSelected x 25%
select 2.1
translateSelected x -25%
the two models end up on top of each other.
Any suggestions?
Thank you.
Jay
From: Robert Hanson <[email protected]<mailto:[email protected]>>
Reply-To:
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Date: Monday, July 23, 2012 1:44 PM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [Jmol-users] trouble with isosurface with Jmol-13.0.RC1
http://chemapps.stolaf.edu/jmol/Jmol-13.zip
On Mon, Jul 23, 2012 at 1:44 PM, Robert Hanson
<[email protected]<mailto:[email protected]>> wrote:
that wouldn't be it. Yes, do check that. Latest is just put up at
http://chemapps.stolaf.edu/jmol/Jmol-13.jar
On Mon, Jul 23, 2012 at 1:41 PM, Shore, Jay
<[email protected]<mailto:[email protected]>> wrote:
Thank you very much Bob.
I think the problem was that I was using "translate x 33% selected"
I wonder if the code was not interpreting the % correctly when opening the
.jmol file.
When I do not use the percent sign, it seems to work.
I will keep on testing.
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: Monday, July 23, 2012 12:11 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, might be a versioning issue there. I think I forgot to upload it.
Please try
http;//chemapps.stolaf.edu/jmol/Jmol-13.zip<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]<mailto:[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]<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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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
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_______________________________________________
Jmol-users mailing list
[email protected]<mailto:[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]<mailto:[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
--
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
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