Re: [Jmol-users] Taxol
Hi Phil, Resolver is currently undergoing some changes. That said, when you query taxol, you’re querying a name unrelated to structure. With Resolver, if you query a SMILES, IUPAC, or InCHI (i.e. identifiers that carry structural information), then Resolver uses CORINA to return 3D coordinates determined by the CORINA algorithm. On the other hand, if you query a non-structural name, then Resolver uses its connections to other databases (PubChem and others) to look-up the 3D structure. Sometimes the returned structure is 2D. I suspect that recent changes at Resolver may have resulted in a change in the taxol look up. Back in 2009, I contacted Markus Sitzmann at NIH regarding Resolver’s response to the “trivial” hexose names. They were not flat, but the stereochemistry was all over the place. I’ll leave you with his quote: “Otis, you’ve discovered Resolver’s weak link - names.” Back then, Markus would correct reported incorrect name look-ups at Resolver’s front door, but doing that would be a full time job in itself. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jan 3, 2016, at 6:15 PM, Philip Bays wrote: > > Observation for both 12.23 and 01.01. When you load taxol from NCl it is not > minimized; it is flat. It did not used to be that way. I suspect it is NCl > since other molecules (cholesterol, tetracycline, etc.) are fine. > > > Philip Bays > Emeritus Professor of Chemistry > Saint Mary's College > Notre Dame, IN 46556 > pb...@saintmarys.edu > > > > -- > ___ > 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] Taxol
Observation for both 12.23 and 01.01. When you load taxol from NCl it is not minimized; it is flat. It did not used to be that way. I suspect it is NCl since other molecules (cholesterol, tetracycline, etc.) are fine. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol defaults for label ?
I was hoping to find a single statement or two that would cause the fault.
Somehow I did not stumble on that. But I also see some other issues so will
get onto those as well.
>From Jamaica,
Bob
On Sun, Jan 3, 2016 at 10:18 AM, Jaime Prilusky <
jaime.prilu...@weizmann.ac.il> wrote:
> See http://proteopedia.org/wiki/tests/tstscene.html
> Click on [scene 2] to load the scene.
> The same scene works Ok after setting some font and alignment attributes
> (find "enabling the following defaults” in the script)
>
> On 3 Jan 2016, at 4:58 PM, Robert Hanson wrote:
>
> Please give me a script I can test.
>
> On Sun, Jan 3, 2016 at 9:57 AM, Jaime Prilusky <
> jaime.prilu...@weizmann.ac.il> wrote:
>
>> Can you please implement defaults again?
>>
>> Jaim
>>
>> On 3 Jan 2016, at 3:33 PM, Robert Hanson wrote:
>>
>> Yes, that's something I changed. Darn. When does it happen?
>>
>> On Sun, Jan 3, 2016 at 6:18 AM, Jaime Prilusky <
>> jaime.prilu...@weizmann.ac.il> wrote:
>>
>>> Unless we set defaults for labels, we get the following JSmol error:
>>> this.colixes is null, when using Jmol 14.4.1 2015-12-23
>>>
>>> Same script works fine with previous 14.3.5_2014.08.09
>>>
>>> Something is not loading as expected?
>>>
>>> Regards,
>>> Jaim
>>>
>>> TypeError: this.colixes is null try/catch path:
>>> 0 function (b,d)
>>> args[0]=TypeError: this.colixes is null
>>> args[1]=function (){a.instantialize(this,arguments)}
>>> 1 JS.ScriptEval.executeCommands(a,b)
>>> args[0]=false
>>> args[1]=true
>>> 2 JS.ScriptEval.evaluateCompiledScript(a,b,c,e,f,p)
>>> args[0]=false
>>> args[1]=false
>>> args[2]=false
>>> args[3]=false
>>> args[4]=null
>>> args[5]=true
>>> 3 JS.ScriptManager.evalStringWaitStatusQueued(a,b,c,e,f)
>>> args[0]=String
>>> args[1]=script ./JournalJBSD1Cv2.spt
>>> args[2]=
>>> args[3]=false
>>> args[4]=true
>>> 4 JV.Viewer.evalStringWaitStatusQueued(a,b,c,g,f)
>>> args[0]=String
>>> args[1]=script ./JournalJBSD1Cv2.spt
>>> args[2]=
>>> args[3]=false
>>> args[4]=true
>>> 5 JS.ScriptQueueThread.runNextScript()
>>> 6 JS.ScriptQueueThread.run1(a)
>>> args[0]=0
>>> 7 J.thread.JmolThread.run()
>>> 8 start()
>>> 9 function ()
>>>
>>> __
>>> Dr Jaime Prilusky
>>> R&D Bioinformatics and Data Management
>>>
>>> Skype: jaime.prilusky.wis
>>> mail: jaime.prilu...@weizmann.ac.il
>>>
>>> OCA, http://oca.weizmann.ac.il (the protein structure/function database)
>>> Proteopedia, http://proteopedia.org (because life has more than 2D)
>>>
>>>
>>>
>>> --
>>>
>>> ___
>>> 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
>>
>>
>>
>>
>> --
>>
>> ___
>> 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
>
>
>
>
> --
>
> ___
> 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.n
[Jmol-users] FirstGlance with 14.4.1_2015.12.23
I have released a new version of FirstGlance in Jmol that uses Jmol 14.4.1_2015.12.23. So far I have found no problems in that version of Jmol that affect FirstGlance. http://FirstGlance.Jmol.Org I have tested browsers: Firefox (best for JSmol!) in OS X and Windows Safari in OS X Chrome in OS X and Windows Internet Explorer in Windows Edge in Windows 10 Opera in OS X and Windows Maxthon in OS X and Windows I tested the Java applet in the browsers that support Java. Browser performance summary: http://bioinformatics.org/firstglance/fgij/notes.htm#browsers Kudos and thanks to Bob and the Jmol community for the continued amazing progress with Jmol!! -Eric -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol defaults for label ?
See http://proteopedia.org/wiki/tests/tstscene.html
Click on [scene 2] to load the scene.
The same scene works Ok after setting some font and alignment attributes (find
"enabling the following defaults” in the script)
On 3 Jan 2016, at 4:58 PM, Robert Hanson
mailto:hans...@stolaf.edu>> wrote:
Please give me a script I can test.
On Sun, Jan 3, 2016 at 9:57 AM, Jaime Prilusky
mailto:jaime.prilu...@weizmann.ac.il>> wrote:
Can you please implement defaults again?
Jaim
On 3 Jan 2016, at 3:33 PM, Robert Hanson
mailto:hans...@stolaf.edu>> wrote:
Yes, that's something I changed. Darn. When does it happen?
On Sun, Jan 3, 2016 at 6:18 AM, Jaime Prilusky
mailto:jaime.prilu...@weizmann.ac.il>> wrote:
Unless we set defaults for labels, we get the following JSmol error:
this.colixes is null, when using Jmol 14.4.1 2015-12-23
Same script works fine with previous 14.3.5_2014.08.09
Something is not loading as expected?
Regards,
Jaim
TypeError: this.colixes is null try/catch path:
0 function (b,d)
args[0]=TypeError: this.colixes is null
args[1]=function (){a.instantialize(this,arguments)}
1 JS.ScriptEval.executeCommands(a,b)
args[0]=false
args[1]=true
2 JS.ScriptEval.evaluateCompiledScript(a,b,c,e,f,p)
args[0]=false
args[1]=false
args[2]=false
args[3]=false
args[4]=null
args[5]=true
3 JS.ScriptManager.evalStringWaitStatusQueued(a,b,c,e,f)
args[0]=String
args[1]=script ./JournalJBSD1Cv2.spt
args[2]=
args[3]=false
args[4]=true
4 JV.Viewer.evalStringWaitStatusQueued(a,b,c,g,f)
args[0]=String
args[1]=script ./JournalJBSD1Cv2.spt
args[2]=
args[3]=false
args[4]=true
5 JS.ScriptQueueThread.runNextScript()
6 JS.ScriptQueueThread.run1(a)
args[0]=0
7 J.thread.JmolThread.run()
8 start()
9 function ()
__
Dr Jaime Prilusky
R&D Bioinformatics and Data Management
Skype: jaime.prilusky.wis
mail: jaime.prilu...@weizmann.ac.il
OCA, http://oca.weizmann.ac.il
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
--
___
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
--
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol defaults for label ?
Please give me a script I can test.
On Sun, Jan 3, 2016 at 9:57 AM, Jaime Prilusky <
jaime.prilu...@weizmann.ac.il> wrote:
> Can you please implement defaults again?
>
> Jaim
>
> On 3 Jan 2016, at 3:33 PM, Robert Hanson wrote:
>
> Yes, that's something I changed. Darn. When does it happen?
>
> On Sun, Jan 3, 2016 at 6:18 AM, Jaime Prilusky <
> jaime.prilu...@weizmann.ac.il> wrote:
>
>> Unless we set defaults for labels, we get the following JSmol error:
>> this.colixes is null, when using Jmol 14.4.1 2015-12-23
>>
>> Same script works fine with previous 14.3.5_2014.08.09
>>
>> Something is not loading as expected?
>>
>> Regards,
>> Jaim
>>
>> TypeError: this.colixes is null try/catch path:
>> 0 function (b,d)
>> args[0]=TypeError: this.colixes is null
>> args[1]=function (){a.instantialize(this,arguments)}
>> 1 JS.ScriptEval.executeCommands(a,b)
>> args[0]=false
>> args[1]=true
>> 2 JS.ScriptEval.evaluateCompiledScript(a,b,c,e,f,p)
>> args[0]=false
>> args[1]=false
>> args[2]=false
>> args[3]=false
>> args[4]=null
>> args[5]=true
>> 3 JS.ScriptManager.evalStringWaitStatusQueued(a,b,c,e,f)
>> args[0]=String
>> args[1]=script ./JournalJBSD1Cv2.spt
>> args[2]=
>> args[3]=false
>> args[4]=true
>> 4 JV.Viewer.evalStringWaitStatusQueued(a,b,c,g,f)
>> args[0]=String
>> args[1]=script ./JournalJBSD1Cv2.spt
>> args[2]=
>> args[3]=false
>> args[4]=true
>> 5 JS.ScriptQueueThread.runNextScript()
>> 6 JS.ScriptQueueThread.run1(a)
>> args[0]=0
>> 7 J.thread.JmolThread.run()
>> 8 start()
>> 9 function ()
>>
>> __
>> Dr Jaime Prilusky
>> R&D Bioinformatics and Data Management
>>
>> Skype: jaime.prilusky.wis
>> mail: jaime.prilu...@weizmann.ac.il
>>
>> OCA, http://oca.weizmann.ac.il (the protein structure/function database)
>> Proteopedia, http://proteopedia.org (because life has more than 2D)
>>
>>
>>
>> --
>>
>> ___
>> 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
>
>
>
>
> --
>
> ___
> 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] JSmol defaults for label ?
Can you please implement defaults again?
Jaim
On 3 Jan 2016, at 3:33 PM, Robert Hanson
mailto:hans...@stolaf.edu>> wrote:
Yes, that's something I changed. Darn. When does it happen?
On Sun, Jan 3, 2016 at 6:18 AM, Jaime Prilusky
mailto:jaime.prilu...@weizmann.ac.il>> wrote:
Unless we set defaults for labels, we get the following JSmol error:
this.colixes is null, when using Jmol 14.4.1 2015-12-23
Same script works fine with previous 14.3.5_2014.08.09
Something is not loading as expected?
Regards,
Jaim
TypeError: this.colixes is null try/catch path:
0 function (b,d)
args[0]=TypeError: this.colixes is null
args[1]=function (){a.instantialize(this,arguments)}
1 JS.ScriptEval.executeCommands(a,b)
args[0]=false
args[1]=true
2 JS.ScriptEval.evaluateCompiledScript(a,b,c,e,f,p)
args[0]=false
args[1]=false
args[2]=false
args[3]=false
args[4]=null
args[5]=true
3 JS.ScriptManager.evalStringWaitStatusQueued(a,b,c,e,f)
args[0]=String
args[1]=script ./JournalJBSD1Cv2.spt
args[2]=
args[3]=false
args[4]=true
4 JV.Viewer.evalStringWaitStatusQueued(a,b,c,g,f)
args[0]=String
args[1]=script ./JournalJBSD1Cv2.spt
args[2]=
args[3]=false
args[4]=true
5 JS.ScriptQueueThread.runNextScript()
6 JS.ScriptQueueThread.run1(a)
args[0]=0
7 J.thread.JmolThread.run()
8 start()
9 function ()
__
Dr Jaime Prilusky
R&D Bioinformatics and Data Management
Skype: jaime.prilusky.wis
mail: jaime.prilu...@weizmann.ac.il
OCA, http://oca.weizmann.ac.il
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
--
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol defaults for label ?
Yes, that's something I changed. Darn. When does it happen?
On Sun, Jan 3, 2016 at 6:18 AM, Jaime Prilusky <
jaime.prilu...@weizmann.ac.il> wrote:
> Unless we set defaults for labels, we get the following JSmol error:
> this.colixes is null, when using Jmol 14.4.1 2015-12-23
>
> Same script works fine with previous 14.3.5_2014.08.09
>
> Something is not loading as expected?
>
> Regards,
> Jaim
>
> TypeError: this.colixes is null try/catch path:
> 0 function (b,d)
> args[0]=TypeError: this.colixes is null
> args[1]=function (){a.instantialize(this,arguments)}
> 1 JS.ScriptEval.executeCommands(a,b)
> args[0]=false
> args[1]=true
> 2 JS.ScriptEval.evaluateCompiledScript(a,b,c,e,f,p)
> args[0]=false
> args[1]=false
> args[2]=false
> args[3]=false
> args[4]=null
> args[5]=true
> 3 JS.ScriptManager.evalStringWaitStatusQueued(a,b,c,e,f)
> args[0]=String
> args[1]=script ./JournalJBSD1Cv2.spt
> args[2]=
> args[3]=false
> args[4]=true
> 4 JV.Viewer.evalStringWaitStatusQueued(a,b,c,g,f)
> args[0]=String
> args[1]=script ./JournalJBSD1Cv2.spt
> args[2]=
> args[3]=false
> args[4]=true
> 5 JS.ScriptQueueThread.runNextScript()
> 6 JS.ScriptQueueThread.run1(a)
> args[0]=0
> 7 J.thread.JmolThread.run()
> 8 start()
> 9 function ()
>
> __
> Dr Jaime Prilusky
> R&D Bioinformatics and Data Management
>
> Skype: jaime.prilusky.wis
> mail: jaime.prilu...@weizmann.ac.il
>
> OCA, http://oca.weizmann.ac.il (the protein structure/function database)
> Proteopedia, http://proteopedia.org (because life has more than 2D)
>
>
>
> --
>
> ___
> 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
[Jmol-users] JSmol defaults for label ?
Unless we set defaults for labels, we get the following JSmol error:
this.colixes is null, when using Jmol 14.4.1 2015-12-23
Same script works fine with previous 14.3.5_2014.08.09
Something is not loading as expected?
Regards,
Jaim
TypeError: this.colixes is null try/catch path:
0 function (b,d)
args[0]=TypeError: this.colixes is null
args[1]=function (){a.instantialize(this,arguments)}
1 JS.ScriptEval.executeCommands(a,b)
args[0]=false
args[1]=true
2 JS.ScriptEval.evaluateCompiledScript(a,b,c,e,f,p)
args[0]=false
args[1]=false
args[2]=false
args[3]=false
args[4]=null
args[5]=true
3 JS.ScriptManager.evalStringWaitStatusQueued(a,b,c,e,f)
args[0]=String
args[1]=script ./JournalJBSD1Cv2.spt
args[2]=
args[3]=false
args[4]=true
4 JV.Viewer.evalStringWaitStatusQueued(a,b,c,g,f)
args[0]=String
args[1]=script ./JournalJBSD1Cv2.spt
args[2]=
args[3]=false
args[4]=true
5 JS.ScriptQueueThread.runNextScript()
6 JS.ScriptQueueThread.run1(a)
args[0]=0
7 J.thread.JmolThread.run()
8 start()
9 function ()
__
Dr Jaime Prilusky
R&D Bioinformatics and Data Management
Skype: jaime.prilusky.wis
mail: jaime.prilu...@weizmann.ac.il
OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)
--
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
