Re: [Jmol-users] Compare Problem (New VersionTest)
On Mon, Aug 24, 2015 at 9:30 PM, Otis Rothenberger osrot...@chemagic.com wrote: Bob, In the world of my small molecule app, I only found these two problems with the new JSmol: 1) The calculate partial charge - MEP special case for alkanes is an easy kludge fix per my previous note. This alkane effect was not present in the older JSmol I was using. that's fixed. It was very simple 2) The compare methane special case is also an easy kludge fix. This was present in the older JSmol. I just missed it because it did not bring up an alert box. The new JSmol version brings up a lengthy JavaScript alert box if you try to compare two methanes. dont kludge. It's fixed kludge is to test for two things before compare. Test for 2 models AND carbon and connected(4,hydrogen)}.length” being equal to 2. Kludge is used here so that I don’t have to use that other term that you don’t like. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Aug 24, 2015, at 8:06 PM, Otis Rothenberger osrot...@chemagic.com wrote: Bob, I should have tested further. It appears that compare is only failing on methane/methane. I guess that I never compared methane to methane before. Once either model is not methane, compare seems to be OK. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Aug 24, 2015, at 1:41 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 08/24/2015 07:33 PM, Robert Hanson wrote: I'll upload a new version and see if that fixes it. I can't tell from this exactly what is going on. Maybe a JS file caching issue? Rolf, you might also make sure your cache is fully cleared. Caching shouldn't be a problem with the 'Jena3D Viewer' because each Jmol version gets its own directory on the server within the URL. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry 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 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Compare Problem (New VersionTest)
Thanks Bob,
I knew I was going to have to un-kludge, but kludging is fun - makes me learn
more Jmol script. I had no idea that you could do this:
{selection}.length
That can come in handy.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Aug 25, 2015, at 7:01 AM, Robert Hanson hans...@stolaf.edu wrote:
On Mon, Aug 24, 2015 at 9:30 PM, Otis Rothenberger osrot...@chemagic.com
mailto:osrot...@chemagic.com wrote:
Bob,
In the world of my small molecule app, I only found these two problems with
the new JSmol:
1) The calculate partial charge - MEP special case for alkanes is an easy
kludge fix per my previous note. This alkane effect was not present in the
older JSmol I was using.
that's fixed. It was very simple
2) The compare methane special case is also an easy kludge fix. This was
present in the older JSmol. I just missed it because it did not bring up an
alert box. The new JSmol version brings up a lengthy JavaScript alert box if
you try to compare two methanes.
dont kludge. It's fixed
kludge is to test for two things before compare. Test for 2 models AND
carbon and connected(4,hydrogen)}.length” being equal to 2.
Kludge is used here so that I don’t have to use that other term that you
don’t like.
Otis
--
Otis Rothenberger
o...@chemagic.com mailto:o...@chemagic.com
http://chemagic.com http://chemagic.com/
On Aug 24, 2015, at 8:06 PM, Otis Rothenberger osrot...@chemagic.com
mailto:osrot...@chemagic.com wrote:
Bob,
I should have tested further. It appears that compare is only failing on
methane/methane. I guess that I never compared methane to methane before.
Once either model is not methane, compare seems to be OK.
Otis
--
Otis Rothenberger
o...@chemagic.com mailto:o...@chemagic.com
http://chemagic.com http://chemagic.com/
On Aug 24, 2015, at 1:41 PM, Rolf Huehne rhue...@fli-leibniz.de
mailto:rhue...@fli-leibniz.de wrote:
On 08/24/2015 07:33 PM, Robert Hanson wrote:
I'll upload a new version and see if that fixes it. I can't tell from this
exactly what is going on. Maybe a JS file caching issue? Rolf, you might
also make sure your cache is fully cleared.
Caching shouldn't be a problem with the 'Jena3D Viewer' because each
Jmol version gets its own directory on the server within the URL.
Regards,
Rolf
--
Rolf Huehne
Postdoc
Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany
Phone: +49 3641 65 6205 tel:%2B49%203641%2065%206205
Fax: +49 3641 65 6210 tel:%2B49%203641%2065%206210
E-Mail: rhue...@fli-leibniz.de mailto:rhue...@fli-leibniz.de
Website: http://www.fli-leibniz.de http://www.fli-leibniz.de/
Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Dennys Klein
VAT No: DE 153 925 464
Register of Associations: No. 230296, Amtsgericht Jena
Tax Number: 162/141/08228
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Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr 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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[Jmol-users] Compare Problem (New VersionTest)
Bob,
Compare goes completely south on me with a lengthy JavaScript error. I’ll paste
my offending script first. This script gets precessed with a Jmol.script() with
2 models in the window:
scpt = 'var i = {*}.atomno.max + 1;var t = {*}.atomno.min;select within(branch,
{atomno=i}, {atomno=t});var x = compare({selected}, {not selected}, ISOMER);’;
scpt += 'var y = These models are + x; if (x == NONE){y = These models do
not have the|same molecular formula!;};y = y.replace(CONFORMATIONAL
,CONFORMATIONAL|).replace(DIASTERIOMERS,DIASTEREOMERS|).replace(,IDENTICAL);set
echo top left; font echo 18 serif; color echo lemonchiffon; echo @y';
Lengthy JavaScript Error Alert
TypeError: null is not an object (evaluating 'c.length') try/catch path:
0 function (b, c)
args[0]=TypeError: null is not an object (evaluating 'c.length')
args[1]=function () {a.instantialize(this,arguments);}
1 JS.SmilesExt.getSmilesCorrelation(a, b, c, e, d, f, j, k, g, h, l, m)
args[0]=0
args[1]=3.4028235e+38
args[2]=null
args[3]=[C1 #1]
args[4]=[]
args[5]=null
args[6]=null
args[7]=false
args[8]=null
args[9]=null
args[10]=false
args[11]=65536
2 JS.MathExt.evaluateCompare(c, a)
args[0]=[JS.ScriptMathProcessor object]
args[1]=Token[bitset(10/0xa) value={{0:4}}][null index =2147483647 i...
3 JS.MathExt.evaluate(c, a, b, d)
args[0]=[JS.ScriptMathProcessor object]
args[1]=Token[keyword(5/0x8101005) value=compare]
args[2]=Token[bitset(10/0xa) value={{0:4}}][null index =2147483647 i...
args[3]=135270405
4 JS.ScriptMathProcessor.evaluateFunction(a)
args[0]=135270405
5 JS.ScriptMathProcessor.addOpAllowMath(a, b, c)
args[0]=Token[keyword(17/0x10100011) value=)]
args[1]=true
args[2]=0
6 JS.ScriptMathProcessor.addOp(a)
args[0]=Token[keyword(17/0x10100011) value=)]
7 JS.ScriptExpr.parameterExpression(a, b, c, e, f, d, h, g, k, n)
args[0]=3
args[1]=16
args[2]=[JS.ScriptMathProcessor object]
args[3]=true
args[4]=0
args[5]=-1
args[6]=1
args[7]=null
args[8]=null
args[9]=false
8 JS.ScriptExpr.setVariable(a, b, c, e)
args[0]=3
args[1]=0
args[2]=x
args[3]=true
9 JS.ScriptEval.cmdSet()
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
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Re: [Jmol-users] Compare Problem (New VersionTest)
I'll upload a new version and see if that fixes it. I can't tell from this exactly what is going on. Maybe a JS file caching issue? Rolf, you might also make sure your cache is fully cleared. Bob -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Compare Problem (New VersionTest)
On 08/24/2015 07:33 PM, Robert Hanson wrote: I'll upload a new version and see if that fixes it. I can't tell from this exactly what is going on. Maybe a JS file caching issue? Rolf, you might also make sure your cache is fully cleared. Caching shouldn't be a problem with the 'Jena3D Viewer' because each Jmol version gets its own directory on the server within the URL. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Compare Problem (New VersionTest)
Bob, I should have tested further. It appears that compare is only failing on methane/methane. I guess that I never compared methane to methane before. Once either model is not methane, compare seems to be OK. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Aug 24, 2015, at 1:41 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 08/24/2015 07:33 PM, Robert Hanson wrote: I'll upload a new version and see if that fixes it. I can't tell from this exactly what is going on. Maybe a JS file caching issue? Rolf, you might also make sure your cache is fully cleared. Caching shouldn't be a problem with the 'Jena3D Viewer' because each Jmol version gets its own directory on the server within the URL. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Compare Problem (New VersionTest)
Bob, In the world of my small molecule app, I only found these two problems with the new JSmol: 1) The calculate partial charge - MEP special case for alkanes is an easy kludge fix per my previous note. This alkane effect was not present in the older JSmol I was using. 2) The compare methane special case is also an easy kludge fix. This was present in the older JSmol. I just missed it because it did not bring up an alert box. The new JSmol version brings up a lengthy JavaScript alert box if you try to compare two methanes. kludge is to test for two things before compare. Test for 2 models AND carbon and connected(4,hydrogen)}.length” being equal to 2. Kludge is used here so that I don’t have to use that other term that you don’t like. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Aug 24, 2015, at 8:06 PM, Otis Rothenberger osrot...@chemagic.com wrote: Bob, I should have tested further. It appears that compare is only failing on methane/methane. I guess that I never compared methane to methane before. Once either model is not methane, compare seems to be OK. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Aug 24, 2015, at 1:41 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 08/24/2015 07:33 PM, Robert Hanson wrote: I'll upload a new version and see if that fixes it. I can't tell from this exactly what is going on. Maybe a JS file caching issue? Rolf, you might also make sure your cache is fully cleared. Caching shouldn't be a problem with the 'Jena3D Viewer' because each Jmol version gets its own directory on the server within the URL. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
