subject:"\[Jmol\-users\] JSmol bug\?"

Re: [Jmol-users] Jsmol bug ?

2015-01-27 Thread Franck Fuster

Yes,  now it works. Well done. Thank you Robert.
Franck
Le 10 janv. 2015 02:12, "Robert Hanson"  a écrit :

> That's a bug. I found the problem; hope to release something this week-end.
>
> On Fri, Jan 9, 2015 at 1:50 PM, Angel Herráez 
> wrote:
>
>> Hi Franck
>>
>> > I have a problem with the mo command in Jsmol : when I want to show
>> > translucent isosurface (with *mo translucent *command) the molecular
>> > orbital is still in opaque.
>>
>> Not sure of your precise problem, but applying tranlucency is some times
>> tricky.
>> Some possible solutions you may try (I cannot tell for sure)
>>
>> Option A:
>> mo color translucent
>> mo color translucent blue
>>
>> Option B:
>> provide the translucent option in another position of the MO command
>>
>> Option C:
>> I often find it safer to apply color and translucency outside of the
>> isosurface command (and
>> MO would behave similarly)
>> So you could try
>> 1. assigning a name-ID to the MO (e.g myMO) -  oh, this may notbe
>> possible but you could
>> use ISOSURFACE MO instead
>> 2. applying color to the object, like:
>> color $myMO translucent
>>
>>
>>
>> ---
>> El software de antivirus Avast ha analizado este correo electrónico en
>> busca de virus.
>> http://www.avast.com
>>
>>
>>
>> --
>> Dive into the World of Parallel Programming! The Go Parallel Website,
>> sponsored by Intel and developed in partnership with Slashdot Media, is
>> your
>> hub for all things parallel software development, from weekly thought
>> leadership blogs to news, videos, case studies, tutorials and more. Take a
>> look and join the conversation now. http://goparallel.sourceforge.net
>> ___
>> 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
>
>
>
> --
> Dive into the World of Parallel Programming! The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot Media, is
> your
> hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials and more. Take a
> look and join the conversation now. http://goparallel.sourceforge.net
> ___
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>
>
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Re: [Jmol-users] Jsmol bug ?

2015-01-09 Thread Robert Hanson

That's a bug. I found the problem; hope to release something this week-end.

On Fri, Jan 9, 2015 at 1:50 PM, Angel Herráez  wrote:

> Hi Franck
>
> > I have a problem with the mo command in Jsmol : when I want to show
> > translucent isosurface (with *mo translucent *command) the molecular
> > orbital is still in opaque.
>
> Not sure of your precise problem, but applying tranlucency is some times
> tricky.
> Some possible solutions you may try (I cannot tell for sure)
>
> Option A:
> mo color translucent
> mo color translucent blue
>
> Option B:
> provide the translucent option in another position of the MO command
>
> Option C:
> I often find it safer to apply color and translucency outside of the
> isosurface command (and
> MO would behave similarly)
> So you could try
> 1. assigning a name-ID to the MO (e.g myMO) -  oh, this may notbe possible
> but you could
> use ISOSURFACE MO instead
> 2. applying color to the object, like:
> color $myMO translucent
>
>
>
> ---
> El software de antivirus Avast ha analizado este correo electrónico en
> busca de virus.
> http://www.avast.com
>
>
>
> --
> Dive into the World of Parallel Programming! The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot Media, is
> your
> hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials and more. Take a
> look and join the conversation now. http://goparallel.sourceforge.net
> ___
> 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
--
Dive into the World of Parallel Programming! The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
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Re: [Jmol-users] Jsmol bug ?

2015-01-09 Thread Angel Herráez

Hi Franck

> I have a problem with the mo command in Jsmol : when I want to show
> translucent isosurface (with *mo translucent *command) the molecular
> orbital is still in opaque.

Not sure of your precise problem, but applying tranlucency is some times tricky.
Some possible solutions you may try (I cannot tell for sure) 

Option A:
mo color translucent
mo color translucent blue

Option B:
provide the translucent option in another position of the MO command

Option C:
I often find it safer to apply color and translucency outside of the isosurface 
command (and 
MO would behave similarly)
So you could try
1. assigning a name-ID to the MO (e.g myMO) -  oh, this may notbe possible but 
you could 
use ISOSURFACE MO instead
2. applying color to the object, like:
color $myMO translucent



---
El software de antivirus Avast ha analizado este correo electrónico en busca de 
virus.
http://www.avast.com


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[Jmol-users] Jsmol bug ?

2015-01-09 Thread Franck Fuster

Good Morning,

I have a problem with the mo command in Jsmol : when I want to show
translucent isosurface (with *mo translucent *command) the molecular
orbital is still in opaque.

I'm using Jsmol 14.3.10_2014.11.27 with chrome Version 39.0.2171.95 or
Firefox Version 39.0.2171.95 m

Did some one have the same problem ?

Best regards

-- 
Franck
--
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Re: [Jmol-users] JSmol bug?

2013-12-16 Thread Robert Hanson

Hmm. That's odd. I was sure I got that right, and it is correct on my
installation. -- one says Jmol 14.0.2 and the other Jmol 14.1.2. In
reality  they are the same. Neither should be showing a "dev" version. You
sure you got that at http://sourceforge.net/projects/jmol/files/ ? I just
downloaded that,  and jsmol/j2s/core/Jmol.properties reads

___JmolDate="$Date: 2013-12-14 11:44:58 -0600 (Sat, 14 Dec 2013) $"
___fullJmolProperties="src/org/jmol/viewer/Jmol.properties"
___JmolVersion="14.0.2"


That URL you give is for Java only, not HTML5, so it's not easy to see what
your problem is.

"JmolCore.js" was a very early attempt, so perhaps you are mixing some old
code with new code.

Bob



On Mon, Dec 16, 2013 at 2:11 PM, Spinney, Richard <
rspin...@chemistry.ohio-state.edu> wrote:

> I have just installed version 14.0.2 (after trying 14.1.2) and both state
> that they are 14.1.1_dev_2013.12.12. It seems to have problems with the
> remarks line in a PDB file (failing to load the molecule), and in JSmol I
> get the error message that JmolCore.js in unavailable, I assume it should
> be JSmolCore.js? I also have a XTY file that seems to load ok but is not
> displayed correctly, the url is:
> https://undergrad-ed.chemistry.ohio-state.edu/H-AOs/2s.html
>
> Rick
> --
> Dr. Richard Spinney
> Department of Chemistry and Biochemistry
> The Ohio State University
> 120A Celeste Laboratory
> 120 West 18th Ave
> Columbus, Ohio 43210
>
> email: rspin...@chemistry.ohio-state.edu
>
> Phone:   (614) 247 - 6847
> Fax:   (614) 292 - 1685
>
>
>
>
> --
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
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>



-- 
Robert M. Hanson
Larson-Anderson Professor 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
--
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[Jmol-users] JSmol bug?

2013-12-16 Thread Spinney, Richard

I have just installed version 14.0.2 (after trying 14.1.2) and both state that 
they are 14.1.1_dev_2013.12.12. It seems to have problems with the remarks line 
in a PDB file (failing to load the molecule), and in JSmol I get the error 
message that JmolCore.js in unavailable, I assume it should be JSmolCore.js? I 
also have a XTY file that seems to load ok but is not displayed correctly, the 
url is: https://undergrad-ed.chemistry.ohio-state.edu/H-AOs/2s.html 

Rick
--
Dr. Richard Spinney
Department of Chemistry and Biochemistry
The Ohio State University
120A Celeste Laboratory
120 West 18th Ave
Columbus, Ohio 43210
 
email: rspin...@chemistry.ohio-state.edu
 
Phone:   (614) 247 - 6847
Fax:   (614) 292 - 1685



--
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Re: [Jmol-users] JSmol bug in reading JVXL files?

2013-05-31 Thread Robert Hanson

Rick,

1) that "error" is just a test we do to check the browsers. You would think
that try/catch would avoid that message, but it doesn't. I don't know why.
Just ignore that.

2) you are probably reading binary files from a local machine or binary
files from a server without having the necessary PHP piece on your server
and pointing to it with Info.serverURL.

No such problem generally. Or tell me my page at
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm doesn't work for you.

Bob



On Fri, May 31, 2013 at 4:13 PM, Spinney, Richard <
rspin...@chemistry.ohio-state.edu> wrote:

>  >This was a Java2Script compiler error. I thought I had worked around
> all of
>
> >those, but this was the first test of old-style JVXL file reading, I
> guess.
>
> >Thanks, Rick!
>
> >** **
>
> >http//chemapps.stolaf.edu/jmol/jsmol.zip
>
> >** **
>
> >Bob
>
> ** **
>
> Thanks Bob, I got the JVXL files working! Unfortunately I have run into
> another problem. I am building a new site using JSmol (an example is
> https://undergrad-ed.chemistry.ohio-state.edu/2310-test/info.php) which
> works great in Firefox. I tested in using Safari and Mercury on an iPad,
> Chrome and IE9 on a PC, and Firefox and Safari on a MacBook (OS 10.8.3) and
> only Firefox on the Macbook works.
>
> ** **
>
> On Chrome I get an error message of “XMLHttpRequest.responseType cannot
> be changed for synchronous HTTP(S) requests made from the window context.”
> And it refers to line 209 in JSmol.min.js. Any help would be appreciated as
> I am lost on this.
>
> ** **
>
> Thanks, Rick
>
> --
>
> Dr. Richard Spinney
>
> Department of Chemistry and Biochemistry
>
> The Ohio State University
>
> 120A Celeste Laboratory
>
> 120 West 18th Ave
>
> Columbus, Ohio 43210
>
>  
>
> email: rspin...@chemistry.ohio-state.edu
>
>  
>
> Phone:   (614) 247 - 6847
>
> Fax:   (614) 292 - 1685
>
> ** **
>
>
> --
> Get 100% visibility into Java/.NET code with AppDynamics Lite
> It's a free troubleshooting tool designed for production
> Get down to code-level detail for bottlenecks, with <2% overhead.
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap2
> ___
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> Jmol-users@lists.sourceforge.net
> 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
--
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Re: [Jmol-users] JSmol bug in reading JVXL files?

2013-05-31 Thread Spinney, Richard

>This was a Java2Script compiler error. I thought I had worked around all of

>those, but this was the first test of old-style JVXL file reading, I guess.

>Thanks, Rick!

>

>http//chemapps.stolaf.edu/jmol/jsmol.zip

>

>Bob

Thanks Bob, I got the JVXL files working! Unfortunately I have run into another 
problem. I am building a new site using JSmol (an example is 
https://undergrad-ed.chemistry.ohio-state.edu/2310-test/info.php) which works 
great in Firefox. I tested in using Safari and Mercury on an iPad, Chrome and 
IE9 on a PC, and Firefox and Safari on a MacBook (OS 10.8.3) and only Firefox 
on the Macbook works.

On Chrome I get an error message of "XMLHttpRequest.responseType cannot be 
changed for synchronous HTTP(S) requests made from the window context." And it 
refers to line 209 in JSmol.min.js. Any help would be appreciated as I am lost 
on this.

Thanks, Rick
--
Dr. Richard Spinney
Department of Chemistry and Biochemistry
The Ohio State University
120A Celeste Laboratory
120 West 18th Ave
Columbus, Ohio 43210

email: 
rspin...@chemistry.ohio-state.edu

Phone:   (614) 247 - 6847
Fax:   (614) 292 - 1685

--
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Re: [Jmol-users] JSmol bug in reading JVXL files?

2013-05-31 Thread Robert Hanson

This was a Java2Script compiler error. I thought I had worked around all of
those, but this was the first test of old-style JVXL file reading, I guess.
Thanks, Rick!

http//chemapps.stolaf.edu/jmol/jsmol.zip

Bob


On Thu, May 30, 2013 at 1:58 PM, Spinney, Richard <
rspin...@chemistry.ohio-state.edu> wrote:

>  I have tracked down the loading error of my script to ‘isosurface plus
> "JVXL/c-2px+.jvxl"; color isosurface opaque blue;’ I get an error message
> of: 
>
> ** **
>
> plus created with cutoff=NaN min=0 max=0; isosurface count: 0
>
> script ERROR: TypeError: this.sg is null J.shapesurface.Isosurface set
> thisID
>
> ** **
>
> This happens when using JSmol in HTML5 mode, version
> 13.1.16_dev_2013.05.28d
>
> ** **
>
> The JAVA version reads this same file without any issues. Any suggestions?
> 
>
> ** **
>
> Thanks, Rick
>
> --
>
> Dr. Richard Spinney
>
> Department of Chemistry and Biochemistry
>
> The Ohio State University
>
> 120A Celeste Laboratory
>
> 120 West 18th Ave
>
> Columbus, Ohio 43210
>
>  
>
> email: rspin...@chemistry.ohio-state.edu
>
>  
>
> Phone:   (614) 247 - 6847
>
> Fax:   (614) 292 - 1685
>
> ** **
>
>
> --
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead
> Download for free and get started troubleshooting in minutes.
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> ___
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> Jmol-users@lists.sourceforge.net
> 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
--
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Re: [Jmol-users] JSmol bug in reading JVXL files?

2013-05-30 Thread Robert Hanson

please send me the file.


On Thu, May 30, 2013 at 1:58 PM, Spinney, Richard <
rspin...@chemistry.ohio-state.edu> wrote:

>  I have tracked down the loading error of my script to ‘isosurface plus
> "JVXL/c-2px+.jvxl"; color isosurface opaque blue;’ I get an error message
> of: 
>
> ** **
>
> plus created with cutoff=NaN min=0 max=0; isosurface count: 0
>
> script ERROR: TypeError: this.sg is null J.shapesurface.Isosurface set
> thisID
>
> ** **
>
> This happens when using JSmol in HTML5 mode, version
> 13.1.16_dev_2013.05.28d
>
> ** **
>
> The JAVA version reads this same file without any issues. Any suggestions?
> 
>
> ** **
>
> Thanks, Rick
>
> --
>
> Dr. Richard Spinney
>
> Department of Chemistry and Biochemistry
>
> The Ohio State University
>
> 120A Celeste Laboratory
>
> 120 West 18th Ave
>
> Columbus, Ohio 43210
>
>  
>
> email: rspin...@chemistry.ohio-state.edu
>
>  
>
> Phone:   (614) 247 - 6847
>
> Fax:   (614) 292 - 1685
>
> ** **
>
>
> --
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap1
> ___
> 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, 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
--
Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
Get 100% visibility into your production application - at no cost.
Code-level diagnostics for performance bottlenecks with <2% overhead
Download for free and get started troubleshooting in minutes.
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Re: [Jmol-users] JSmol bug?

2013-05-17 Thread Bob Hanson

Test2.htm doesn't use controls. See testcb.htm in most recent version. 
JSmolControls.js

Sent from my stupid iPhone 

On May 17, 2013, at 8:44 AM, "Spinney, Richard" 
 wrote:

> I have been trying to get JSmol to work and have had a couple of problems. I 
> have a page (build off of the test2.htm demo) that uses the Java applet 
> (https://undergrad-ed.chemistry.ohio-state.edu/2310-test/info.php) , while 
> this displays the PDB and JVXL files correctly, the controls do not appear. I 
> get an error message of “error Jmol.controls undefined” and links to 
> JSmolApi.js. These lead to lines in the code of: “return 
> Jmol.controls._getMenu(….)”; and “return Jmol.control._getCheckbox(…)”.
>  
> I copied this page 
> (https://undergrad-ed.chemistry.ohio-state.edu/2310-test/info-b.php) and 
> changed it to use HTML5 (JSmol.min.js). Again the PDB files are read ok but 
> now the JVXL files don’t work while the controls (menu and checkboxs) do 
> work. The error message on this is “g._applet is null” and points to the 
> JSmol.min.js file.
>  
> I am at a loss on what is wrong here; the calls to the controls are identical 
> between the two pages, as are the load JVXL calls. It does use the serverURL 
> to call jsmol.php and it is version 13.1.16_dev_2013.5.15. Any help would be 
> appreciated.
>  
> Thanks, Rick
> --
> Dr. Richard Spinney
> Department of Chemistry and Biochemistry
> The Ohio State University
> 120A Celeste Laboratory
> 120 West 18th Ave
> Columbus, Ohio 43210
>  
> email: rspin...@chemistry.ohio-state.edu
>  
> Phone:   (614) 247 - 6847
> Fax:   (614) 292 - 1685
>  
> --
> AlienVault Unified Security Management (USM) platform delivers complete
> security visibility with the essential security capabilities. Easily and
> efficiently configure, manage, and operate all of your security controls
> from a single console and one unified framework. Download a free trial.
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[Jmol-users] JSmol bug?

2013-05-17 Thread Spinney, Richard

I have been trying to get JSmol to work and have had a couple of problems. I 
have a page (build off of the test2.htm demo) that uses the Java applet 
(https://undergrad-ed.chemistry.ohio-state.edu/2310-test/info.php) , while this 
displays the PDB and JVXL files correctly, the controls do not appear. I get an 
error message of "error Jmol.controls undefined" and links to JSmolApi.js. 
These lead to lines in the code of: "return Jmol.controls._getMenu()"; and 
"return Jmol.control._getCheckbox(...)".

I copied this page 
(https://undergrad-ed.chemistry.ohio-state.edu/2310-test/info-b.php) and 
changed it to use HTML5 (JSmol.min.js). Again the PDB files are read ok but now 
the JVXL files don't work while the controls (menu and checkboxs) do work. The 
error message on this is "g._applet is null" and points to the JSmol.min.js 
file.

I am at a loss on what is wrong here; the calls to the controls are identical 
between the two pages, as are the load JVXL calls. It does use the serverURL to 
call jsmol.php and it is version 13.1.16_dev_2013.5.15. Any help would be 
appreciated.

Thanks, Rick
--
Dr. Richard Spinney
Department of Chemistry and Biochemistry
The Ohio State University
120A Celeste Laboratory
120 West 18th Ave
Columbus, Ohio 43210

email: 
rspin...@chemistry.ohio-state.edu

Phone:   (614) 247 - 6847
Fax:   (614) 292 - 1685

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[Jmol-users] JSmol bug?

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