Re: [Jmol-users] Drawing Options

[Andreas Prlic]

I'm running Jmol 12.0.22 through BioJava.

> We need to get BioJava gurus to move to Jmol 13. (Andreas? Peter?) Maybe
> there is a newer version of BioJava than what you are using.
>
>
Good point. - I upgraded the BioJava to the latest Jmol version that is
available from Maven central - 13.0.10. Having Jmol now in Maven central
makes upgrades so much easier!

Andreas
--
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Re: [Jmol-users] Transfer show info from JSO to Javascript?

[Robert Hanson]

http://chemapps.stolaf.edu/jmol/docs/?&search=quaternion%28%29#jmolmath

*The quaternion q = quaternion(script("show rotation")) (or, in Jmol 12.2,
just q = quaternion()) measures how much the model has been rotated from
its reference position (with x to the right, y to the top, and z toward the
user). It can be used to align any axis or plane with any other
"window-frame" axis. For example, here is a quaternion recipe for the
shortest rotation that takes atom "X" and puts it between the center of the
model and the user, that is, "in the forefront:"*

*q = quaternion(script("show rotation"))
toAtom = {C1}.xyz - {*}.xyz
toUser = (!q)%{0 0 1}
axis = cross(toAtom, toUser)
a = angle(toAtom, {0 0 0}, axis, toUser)
rotate MOLECULAR {0 0 0} @axis @a
*


On Fri, Feb 22, 2013 at 5:34 PM, Dan Kirshner wrote:

> Excellent, thanks.
>
> But where is it that I can learn that there such a thing as "quaternion()"?
>
> --Dan
>
>
>   --
> *From:* Robert Hanson 
> *To:* "jmol-users@lists.sourceforge.net" 
>
> *Sent:* Friday, February 22, 2013 1:47 PM
> *Subject:* Re: [Jmol-users] Transfer show info from JSO to Javascript?
>
> sure, but
>
> quaternion()
>
> should do the same thing -- and we should think about the fact that with
> JSmol we don't need conversion from Java classes, since everything is
> JavaScript!
>
> Bob
>
>
>
> On Fri, Feb 22, 2013 at 1:51 PM, Paul Pillot <
> paul.pil...@ac-orleans-tours.fr> wrote:
>
> Jmol.evaluate(myJmol1,"script(show orientation)") will do !
> -Paul
>
> Le 22 févr. 2013 à 20:27, Dan Kirshner a écrit :
>
> Sorry, I'm just not getting how to do this.
>
> I'd like to get the quaternion info for the current model rotation and
> manipulate it in Javascript.
>
> I'm using the Jmol Javascript Object.  I'm happily running scripts with
> something like
>
>var script = "";
>Jmol.script (myJmol1, script);
>
> The Jmol command
>
>show orientation rotation;
>
> gives me the numbers I want -- in both the Jmol Script Console and in the
> Java Console.
>
> How do I get these numbers into a Javascript variable?
>
> Something like
>
>var q = Jmol.getInfo (myJmol1, "show orientation rotation");
>
> is what I'm thinking, but I haven't found a variation that works!
>
> Thanks!
>
> --Dan
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
>
> http://p.sf.net/sfu/appdyn_d2d_feb___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> ___
> 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
>
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> ___
> 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
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
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Re: [Jmol-users] Drawing Options

[Robert Hanson]

On Fri, Feb 22, 2013 at 5:23 PM, Spencer Bliven  wrote:

> I've been trying to customized some jmol scripts and I had a couple
> questions.
>
>1. Is there an option to change the length of the arrowhead for a
>'draw arrow' or 'draw arrow arc' command?
>
>
size overall, but not length per se.


 set defaultDrawArrowScale (decimal)

*Sets the default scale for the arrow tip for
arrows.
*




>
>1. What are the units for the 'scale' parameter for an arc? I've found
>that a value of 500 results in an arc about 1A in radius for my test
>protein, but I assume this is somehow proportionate to the input points.
>
>
*The SCALE parameter is used to set the diameter of the overall circle
containing the arc. *

draw scale 2.0 arc 2-Angstrom diameter
draw scale 500 arc ... 5-Angstrom diameter


>1. What's the best way to draw a line without an arrow head? Use 'draw
>cylinder'?
>
> Yes, I think so.


> I'm running Jmol 12.0.22 through BioJava.
>
We need to get BioJava gurus to move to Jmol 13. (Andreas? Peter?) Maybe
there is a newer version of BioJava than what you are using.


> I have to say that the 
> documentationfor the draw command 
> is rather confusing, since some of the "modifying
> options" are mutually exclusive or  change meanings depending on other
> options.
>

Probably in need of an upgrade.


> Thanks,
>
> Spencer Bliven
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> ___
> 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
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
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Re: [Jmol-users] Transfer show info from JSO to Javascript?

[N David Brown]

http://chemapps.stolaf.edu/jmol/docs/


On 22 February 2013 23:34, Dan Kirshner  wrote:

> Excellent, thanks.
>
> But where is it that I can learn that there such a thing as "quaternion()"?
>
> --Dan
>
>
>   --
> *From:* Robert Hanson 
> *To:* "jmol-users@lists.sourceforge.net" 
>
> *Sent:* Friday, February 22, 2013 1:47 PM
> *Subject:* Re: [Jmol-users] Transfer show info from JSO to Javascript?
>
> sure, but
>
> quaternion()
>
> should do the same thing -- and we should think about the fact that with
> JSmol we don't need conversion from Java classes, since everything is
> JavaScript!
>
> Bob
>
>
>
> On Fri, Feb 22, 2013 at 1:51 PM, Paul Pillot <
> paul.pil...@ac-orleans-tours.fr> wrote:
>
> Jmol.evaluate(myJmol1,"script(show orientation)") will do !
> -Paul
>
> Le 22 févr. 2013 à 20:27, Dan Kirshner a écrit :
>
> Sorry, I'm just not getting how to do this.
>
> I'd like to get the quaternion info for the current model rotation and
> manipulate it in Javascript.
>
> I'm using the Jmol Javascript Object.  I'm happily running scripts with
> something like
>
>var script = "";
>Jmol.script (myJmol1, script);
>
> The Jmol command
>
>show orientation rotation;
>
> gives me the numbers I want -- in both the Jmol Script Console and in the
> Java Console.
>
> How do I get these numbers into a Javascript variable?
>
> Something like
>
>var q = Jmol.getInfo (myJmol1, "show orientation rotation");
>
> is what I'm thinking, but I haven't found a variation that works!
>
> Thanks!
>
> --Dan
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
>
> http://p.sf.net/sfu/appdyn_d2d_feb___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> ___
> 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
>
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
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Re: [Jmol-users] Transfer show info from JSO to Javascript?

[Dan Kirshner]

Excellent, thanks.

But where is it that I can learn that there such a thing as "quaternion()"?

--Dan




>
> From: Robert Hanson 
>To: "jmol-users@lists.sourceforge.net"  
>Sent: Friday, February 22, 2013 1:47 PM
>Subject: Re: [Jmol-users] Transfer show info from JSO to Javascript?
> 
>
>sure, but 
>
>quaternion()
>
>should do the same thing -- and we should think about the fact that with JSmol 
>we don't need conversion from Java classes, since everything is JavaScript!
>
>Bob
>
>
>
>
>
>On Fri, Feb 22, 2013 at 1:51 PM, Paul Pillot  
>wrote:
>
>Jmol.evaluate(myJmol1,"script(show orientation)") will do !
>>-Paul
>>
>>
>>
>>Le 22 févr. 2013 à 20:27, Dan Kirshner a écrit :
>>
>>Sorry, I'm just not getting how to do this.
>>>
>>>
>>>I'd like to get the quaternion info for the current model rotation and 
>>>manipulate it in Javascript.
>>>
>>>
>>>I'm using the Jmol Javascript Object.  I'm happily running scripts with 
>>>something like
>>>
>>>
>>>   var script = "";
>>>
>>>   Jmol.script (myJmol1, script);
>>>
>>>
>>>The Jmol command
>>>
>>>
>>>   show orientation rotation;
>>>
>>>
>>>gives me the numbers I want -- in both the Jmol Script Console and in the 
>>>Java Console.
>>>
>>>
>>>How do I get these numbers into a Javascript variable?
>>>
>>>
>>>Something like
>>>
>>>
>>>   var q = Jmol.getInfo (myJmol1, "show orientation rotation");
>>>
>>>
>>>is what I'm thinking, but I haven't found a variation that works!
>>>
>>>
>>>Thanks!
>>>
>>>
>>>--Dan
>>>
>>>
>>>
>>>--
>>>Everyone hates slow websites. So do we.
>>>Make your web apps faster with AppDynamics
>>>Download AppDynamics Lite for free today:
>>>http://p.sf.net/sfu/appdyn_d2d_feb___
>>>Jmol-users mailing list
>>>Jmol-users@lists.sourceforge.net
>>>https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>
>>--
>>Everyone hates slow websites. So do we.
>>Make your web apps faster with AppDynamics
>>Download AppDynamics Lite for free today:
>>http://p.sf.net/sfu/appdyn_d2d_feb
>>___
>>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
>
>
>--
>Everyone hates slow websites. So do we.
>Make your web apps faster with AppDynamics
>Download AppDynamics Lite for free today:
>http://p.sf.net/sfu/appdyn_d2d_feb
>___
>Jmol-users mailing list
>Jmol-users@lists.sourceforge.net
>https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb___
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[Jmol-users] Drawing Options

[Spencer Bliven]

I've been trying to customized some jmol scripts and I had a couple
questions.

   1. Is there an option to change the length of the arrowhead for a 'draw
   arrow' or 'draw arrow arc' command?
   2. What are the units for the 'scale' parameter for an arc? I've found
   that a value of 500 results in an arc about 1A in radius for my test
   protein, but I assume this is somehow proportionate to the input points.
   3. What's the best way to draw a line without an arrow head? Use 'draw
   cylinder'?

I'm running Jmol 12.0.22 through BioJava.

I have to say that the
documentationfor the draw
command is rather confusing, since some of the "modifying
options" are mutually exclusive or  change meanings depending on other
options.

Thanks,

Spencer Bliven
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
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Re: [Jmol-users] WebMO

[Robert Hanson]

Java is back working on Safari. I realize it's tough going up against an
institution like Homeland Security. Browsers are now set up to ask first if
you want access, and that seems to me a more reasoned response.


On Fri, Feb 22, 2013 at 2:09 PM, Jennifer L. Muzyka <
jennifer.muz...@centre.edu> wrote:

> Bob,
> Java has been disabled on all campus computers at Centre.  I think
> Centre's response is pretty reasonable, given that Homeland Security
> recommends disabling Java.  See the article the ITS folks shared with me:
> http://www.informationweek.com/security/vulnerabilities/10-facts-secure-java-for-business-use/240146322
>
> <
> http://www.informationweek.com/security/vulnerabilities/10-facts-secure-java-for-business-use/240146322
> >
> In addition to Centre and Homeland Security, many of the browser
> manufacturers are disabling Java so users don't have much choice.  I think
> Apple has done that with Safari (which I don't use).  I'm especially
> thrilled about the existence of JSmol.  It's very timely.
> Jennifer
>
>
>
>
> On Feb 22, 2013, at 2:51 PM,  >
>  wrote:
>
> --
>
> Message: 1
> Date: Fri, 22 Feb 2013 13:16:17 -0600
> From: Robert Hanson mailto:hans...@stolaf.edu>>
> Subject: Re: [Jmol-users] WebMO
> To: "jmol-users@lists.sourceforge.net jmol-users@lists.sourceforge.net>"
> mailto:jmol-users@lists.sourceforge.net
> >>
> Message-ID:
>   >>
> Content-Type: text/plain; charset="iso-8859-1"
>
> No sign of that yet.
>
> Is there a reason you do not have Java in your teaching labs? Is this just
> an IT department crack-down? St. Olaf is still supporting Java
>
>
> On Fri, Feb 22, 2013 at 12:08 PM, Jennifer L. Muzyka <
> jennifer.muz...@centre.edu> wrote:
>
> Does anybody know about a JSmol version of WebMO?  We're going to have
> trouble doing computational chemistry experiments in our teaching labs
> without Java, since we use WebMO.  I would appreciate any information or
> insights anybody can offer.  Thanks.
> Jennifer
>
>
>
>
>
> Jennifer L. Muzyka
> Professor of Chemistry
> Centre College
> 600 West Walnut Street
> Danville, KY  40422
>
> jennifer.muz...@centre.edu
> http://web.centre.edu/muzyka/
>
>
>
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> ___
> 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
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb___
Jmol-users mailing list
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Re: [Jmol-users] Transfer show info from JSO to Javascript?

[Robert Hanson]

sure, but

quaternion()

should do the same thing -- and we should think about the fact that with
JSmol we don't need conversion from Java classes, since everything is
JavaScript!

Bob



On Fri, Feb 22, 2013 at 1:51 PM, Paul Pillot <
paul.pil...@ac-orleans-tours.fr> wrote:

> Jmol.evaluate(myJmol1,"script(show orientation)") will do !
> -Paul
>
> Le 22 févr. 2013 à 20:27, Dan Kirshner a écrit :
>
> Sorry, I'm just not getting how to do this.
>
> I'd like to get the quaternion info for the current model rotation and
> manipulate it in Javascript.
>
> I'm using the Jmol Javascript Object.  I'm happily running scripts with
> something like
>
>var script = "";
>Jmol.script (myJmol1, script);
>
> The Jmol command
>
>show orientation rotation;
>
> gives me the numbers I want -- in both the Jmol Script Console and in the
> Java Console.
>
> How do I get these numbers into a Javascript variable?
>
> Something like
>
>var q = Jmol.getInfo (myJmol1, "show orientation rotation");
>
> is what I'm thinking, but I haven't found a variation that works!
>
> Thanks!
>
> --Dan
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
>
> http://p.sf.net/sfu/appdyn_d2d_feb___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> ___
> 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
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] WebMO

[Jennifer L. Muzyka]

Mike,
Thanks for checking on the latest WebMO update.  I contacted them and they say 
there's no way all that complex Java stuff can be done with JavaScript.  On my 
reply, I copied Bob Hanson.  He responded with details about JSmol that will 
hopefully get the WebMO folks thinking about the topic.  In the meantime, maybe 
we can get ITS to let us use a little bit of Java on campus.

Centre's campus has changed a bit since you were here in 2003.  Let me know if 
you are here on campus and would like a tour of the chemistry facilities.
Jennifer



On Feb 22, 2013, at 1:14 PM, jmol-users-requ...@lists.sourceforge.net wrote:
> 
> --
> 
> Message: 3
> Date: Fri, 22 Feb 2013 12:14:33 -0600
> From: Michael Evans 
> Subject: Re: [Jmol-users] WebMO
> To: "jmol-users@lists.sourceforge.net"
>   
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Jennifer,
> Looks like the last update to WebMO was in August 2012. Perhaps a version
> employing JSMol is in the works? Not sure. I don't see any reason why it
> shouldn't be possible...Jmol just reads the output of WebMO calculations;
> it doesn't do any of the calculations itself.
> 
> BTW, I lived at Centre for the Governor's Scholars Program back in 2003.
> Hard to believe it's been ten years since then...I'm sure the campus is as
> beautiful as ever!
> 
> Cheers, Mike
> 
> 
> ---
> Michael Evans
> Department of Chemistry
> University of Illinois, Urbana-Champaign
> 
> 
> On Fri, Feb 22, 2013 at 12:08 PM, Jennifer L. Muzyka <
> jennifer.muz...@centre.edu> wrote:
> 
>> Does anybody know about a JSmol version of WebMO?  We're going to have
>> trouble doing computational chemistry experiments in our teaching labs
>> without Java, since we use WebMO.  I would appreciate any information or
>> insights anybody can offer.  Thanks.
>> Jennifer
>> 
>> 
>> 
>> 
>> 
>> Jennifer L. Muzyka
>> Professor of Chemistry
>> Centre College
>> 600 West Walnut Street
>> Danville, KY  40422
>> 
>> jennifer.muz...@centre.edu
>> http://web.centre.edu/muzyka/
>> 
>> 
>> 
> **

Jennifer L. Muzyka
Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka/




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Re: [Jmol-users] WebMO

[Jennifer L. Muzyka]

Bob,
Java has been disabled on all campus computers at Centre.  I think Centre's 
response is pretty reasonable, given that Homeland Security recommends 
disabling Java.  See the article the ITS folks shared with me:  
http://www.informationweek.com/security/vulnerabilities/10-facts-secure-java-for-business-use/240146322


In addition to Centre and Homeland Security, many of the browser manufacturers 
are disabling Java so users don't have much choice.  I think Apple has done 
that with Safari (which I don't use).  I'm especially thrilled about the 
existence of JSmol.  It's very timely.
Jennifer




On Feb 22, 2013, at 2:51 PM, 
mailto:jmol-users-requ...@lists.sourceforge.net>>
 wrote:

--

Message: 1
Date: Fri, 22 Feb 2013 13:16:17 -0600
From: Robert Hanson mailto:hans...@stolaf.edu>>
Subject: Re: [Jmol-users] WebMO
To: "jmol-users@lists.sourceforge.net"
mailto:jmol-users@lists.sourceforge.net>>
Message-ID:
mailto:caf_yuvutvpukm1sseq12w3kt2sg1fs6mn-pwbcljnawo2di...@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"

No sign of that yet.

Is there a reason you do not have Java in your teaching labs? Is this just
an IT department crack-down? St. Olaf is still supporting Java


On Fri, Feb 22, 2013 at 12:08 PM, Jennifer L. Muzyka <
jennifer.muz...@centre.edu> wrote:

Does anybody know about a JSmol version of WebMO?  We're going to have
trouble doing computational chemistry experiments in our teaching labs
without Java, since we use WebMO.  I would appreciate any information or
insights anybody can offer.  Thanks.
Jennifer





Jennifer L. Muzyka
Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka/




--
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Re: [Jmol-users] Transfer show info from JSO to Javascript?

[Robert Hanson]

var q = Jmol.evaluate(myJmol, "quaternion()")




On Fri, Feb 22, 2013 at 1:27 PM, Dan Kirshner wrote:

> Sorry, I'm just not getting how to do this.
>
> I'd like to get the quaternion info for the current model rotation and
> manipulate it in Javascript.
>
> I'm using the Jmol Javascript Object.  I'm happily running scripts with
> something like
>
>var script = "";
>Jmol.script (myJmol1, script);
>
> The Jmol command
>
>show orientation rotation;
>
> gives me the numbers I want -- in both the Jmol Script Console and in the
> Java Console.
>
> How do I get these numbers into a Javascript variable?
>
> Something like
>
>var q = Jmol.getInfo (myJmol1, "show orientation rotation");
>
> is what I'm thinking, but I haven't found a variation that works!
>
> Thanks!
>
> --Dan
>
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> ___
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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] Transfer show info from JSO to Javascript?

[Paul Pillot]

Jmol.evaluate(myJmol1,"script(show orientation)") will do !
-Paul

Le 22 févr. 2013 à 20:27, Dan Kirshner a écrit :

> Sorry, I'm just not getting how to do this.
> 
> I'd like to get the quaternion info for the current model rotation and 
> manipulate it in Javascript.
> 
> I'm using the Jmol Javascript Object.  I'm happily running scripts with 
> something like
> 
>var script = "";
>Jmol.script (myJmol1, script);
> 
> The Jmol command
> 
>show orientation rotation;
> 
> gives me the numbers I want -- in both the Jmol Script Console and in the 
> Java Console.
> 
> How do I get these numbers into a Javascript variable?
> 
> Something like
> 
>var q = Jmol.getInfo (myJmol1, "show orientation rotation");
> 
> is what I'm thinking, but I haven't found a variation that works!
> 
> Thanks!
> 
> --Dan
> 
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

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[Jmol-users] Transfer show info from JSO to Javascript?

[Dan Kirshner]

Sorry, I'm just not getting how to do this.

I'd like to get the quaternion info for the current model rotation and 
manipulate it in Javascript.

I'm using the Jmol Javascript Object.  I'm happily running scripts with 
something like

   var script = "";

   Jmol.script (myJmol1, script);

The Jmol command

   show orientation rotation;

gives me the numbers I want -- in both the Jmol Script Console and in the Java 
Console.

How do I get these numbers into a Javascript variable?

Something like

   var q = Jmol.getInfo (myJmol1, "show orientation rotation");

is what I'm thinking, but I haven't found a variation that works!

Thanks!

--Dan--
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Re: [Jmol-users] WebMO

[Robert Hanson]

No sign of that yet.

Is there a reason you do not have Java in your teaching labs? Is this just
an IT department crack-down? St. Olaf is still supporting Java


On Fri, Feb 22, 2013 at 12:08 PM, Jennifer L. Muzyka <
jennifer.muz...@centre.edu> wrote:

> Does anybody know about a JSmol version of WebMO?  We're going to have
> trouble doing computational chemistry experiments in our teaching labs
> without Java, since we use WebMO.  I would appreciate any information or
> insights anybody can offer.  Thanks.
> Jennifer
>
>
>
>
>
> Jennifer L. Muzyka
> Professor of Chemistry
> Centre College
> 600 West Walnut Street
> Danville, KY  40422
>
> jennifer.muz...@centre.edu
> http://web.centre.edu/muzyka/
>
>
>
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> ___
> 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
--
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Re: [Jmol-users] WebMO

[Michael Evans]

Jennifer,
Looks like the last update to WebMO was in August 2012. Perhaps a version
employing JSMol is in the works? Not sure. I don't see any reason why it
shouldn't be possible...Jmol just reads the output of WebMO calculations;
it doesn't do any of the calculations itself.

BTW, I lived at Centre for the Governor's Scholars Program back in 2003.
Hard to believe it's been ten years since then...I'm sure the campus is as
beautiful as ever!

Cheers, Mike


---
Michael Evans
Department of Chemistry
University of Illinois, Urbana-Champaign


On Fri, Feb 22, 2013 at 12:08 PM, Jennifer L. Muzyka <
jennifer.muz...@centre.edu> wrote:

> Does anybody know about a JSmol version of WebMO?  We're going to have
> trouble doing computational chemistry experiments in our teaching labs
> without Java, since we use WebMO.  I would appreciate any information or
> insights anybody can offer.  Thanks.
> Jennifer
>
>
>
>
>
> Jennifer L. Muzyka
> Professor of Chemistry
> Centre College
> 600 West Walnut Street
> Danville, KY  40422
>
> jennifer.muz...@centre.edu
> http://web.centre.edu/muzyka/
>
>
>
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
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[Jmol-users] WebMO

[Jennifer L. Muzyka]

Does anybody know about a JSmol version of WebMO?  We're going to have trouble 
doing computational chemistry experiments in our teaching labs without Java, 
since we use WebMO.  I would appreciate any information or insights anybody can 
offer.  Thanks.
Jennifer





Jennifer L. Muzyka
Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka/




--
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Re: [Jmol-users] Problem with switching to JSMol

[Robert Hanson]

email is fine. I have time today to look at it. I'm sure it will only take
a few minutes.


On Fri, Feb 22, 2013 at 11:53 AM, Simone Sturniolo <
simonesturni...@gmail.com> wrote:

> It's a bit of a big thing. 5 MB at least I'd say, all things included. How
> do you prefer me to send it?
>
> Simone
>
>
> 2013/2/22 Robert Hanson 
>
>> If you send me a copy of the page or a link to it, I can help you track
>> this down. Something simple, I'm sure.
>>
>>
>> On Fri, Feb 22, 2013 at 6:46 AM, Simone Sturniolo <
>> simonesturni...@gmail.com> wrote:
>>
>>> Tried that. Every other order either increases the number of error
>>> messages, or leaves the situation unchanged.
>>>
>>>
>>> 2013/2/22 Paul Pillot 
>>>
 Order matters in your js files links
 I use the following declaration:
  
 

 That is with the minified version and without webGL.
 Paul

 Le 22 févr. 2013 à 12:43, Simone Sturniolo a écrit :

 Hi,

 I'm trying to switch my JMol applet web page to JSMol - mainly to avoid
 all the problems related with ever increasing restrictive security policies
 for Java. I put all the main JSMol files in a folder, j2s in a subfolder,
 loaded the scripts:

 
 
 
 >>> src="jsmol/JSmolControls.js">
 
 
 
 
 
 

 completed the info section as follows:

 var main_info = {
  width: jmolW,
  height: jmolH,
  addSelectionOptions: false,
  color: "#00",
  debug: false,
  defaultModel: "",
  memoryLimit: 512,
  readyFunction: null,
  script: "",
  use: "HTML5",
  j2sPath: "jsmol/j2s",
  serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php";,
  console: "myJmol_infodiv",
  scriptCallback: "afterscript_callback",
  loadStructCallback: "afterload_callback",
  pickCallback: "pick_callback",
  src: null,
 }

 left the rest of the code unchanged, basically following the
 instructions found on http://wiki.jmol.org/index.php/JSmol, and now am
 running the thing on Firefox 18.0.2. I get this error:

 TypeError: Jmol._getElement(...).style is undefined

 Jmol._getElement(this, "infotablediv").style.display = (tf ? "block" : 
 "none");

 JSmol.js (line 395)

 What could be causing this, and what did I forget to do?
 Thank you very much!

 Simone



 --
 ___

 Nuovo indirizzo e-mail:
 simonesturni...@gmail.com

 --
 Everyone hates slow websites. So do we.
 Make your web apps faster with AppDynamics
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 http://p.sf.net/sfu/appdyn_d2d_feb___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users




 --
 Everyone hates slow websites. So do we.
 Make your web apps faster with AppDynamics
 Download AppDynamics Lite for free today:
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 ___
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 https://lists.sourceforge.net/lists/listinfo/jmol-users


>>>
>>>
>>> --
>>> ___
>>>
>>> Nuovo indirizzo e-mail:
>>> simonesturni...@gmail.com
>>>
>>>
>>> --
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_feb
>>> ___
>>> 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
>>
>>
>>
>> --
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_feb
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> ___
>
> Nuovo indirizzo e-mail:
> simonesturni...@gmail.com
>
>
> --

Re: [Jmol-users] Problem with switching to JSMol

[Simone Sturniolo]

It's a bit of a big thing. 5 MB at least I'd say, all things included. How
do you prefer me to send it?

Simone


2013/2/22 Robert Hanson 

> If you send me a copy of the page or a link to it, I can help you track
> this down. Something simple, I'm sure.
>
>
> On Fri, Feb 22, 2013 at 6:46 AM, Simone Sturniolo <
> simonesturni...@gmail.com> wrote:
>
>> Tried that. Every other order either increases the number of error
>> messages, or leaves the situation unchanged.
>>
>>
>> 2013/2/22 Paul Pillot 
>>
>>> Order matters in your js files links
>>> I use the following declaration:
>>>  
>>> 
>>>
>>> That is with the minified version and without webGL.
>>> Paul
>>>
>>> Le 22 févr. 2013 à 12:43, Simone Sturniolo a écrit :
>>>
>>> Hi,
>>>
>>> I'm trying to switch my JMol applet web page to JSMol - mainly to avoid
>>> all the problems related with ever increasing restrictive security policies
>>> for Java. I put all the main JSMol files in a folder, j2s in a subfolder,
>>> loaded the scripts:
>>>
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>>
>>> completed the info section as follows:
>>>
>>> var main_info = {
>>>  width: jmolW,
>>>  height: jmolH,
>>>  addSelectionOptions: false,
>>>  color: "#00",
>>>  debug: false,
>>>  defaultModel: "",
>>>  memoryLimit: 512,
>>>  readyFunction: null,
>>>  script: "",
>>>  use: "HTML5",
>>>  j2sPath: "jsmol/j2s",
>>>  serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php";,
>>>  console: "myJmol_infodiv",
>>>  scriptCallback: "afterscript_callback",
>>>  loadStructCallback: "afterload_callback",
>>>  pickCallback: "pick_callback",
>>>  src: null,
>>> }
>>>
>>> left the rest of the code unchanged, basically following the
>>> instructions found on http://wiki.jmol.org/index.php/JSmol, and now am
>>> running the thing on Firefox 18.0.2. I get this error:
>>>
>>> TypeError: Jmol._getElement(...).style is undefined
>>>
>>> Jmol._getElement(this, "infotablediv").style.display = (tf ? "block" : 
>>> "none");
>>>
>>> JSmol.js (line 395)
>>>
>>> What could be causing this, and what did I forget to do?
>>> Thank you very much!
>>>
>>> Simone
>>>
>>>
>>>
>>> --
>>> ___
>>>
>>> Nuovo indirizzo e-mail:
>>> simonesturni...@gmail.com
>>>
>>> --
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>>
>>> http://p.sf.net/sfu/appdyn_d2d_feb___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>>
>>>
>>> --
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_feb
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> --
>> ___
>>
>> Nuovo indirizzo e-mail:
>> simonesturni...@gmail.com
>>
>>
>> --
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_feb
>> ___
>> 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
>
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
___

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[Jmol-users] unsubscrube

[Mochena, Mogus D.]

-Original Message-
From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: Fri 2/22/2013 11:59 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Jmol 13.1.13 released - several new features
 
On Fri, Feb 22, 2013 at 3:49 AM, Egon Willighagen <
egon.willigha...@gmail.com> wrote:

> On Fri, Feb 22, 2013 at 1:27 AM, Robert Hanson  wrote:
> > Most notably, Jmol 13.1.13 reads PyMOL session files (.PSE). There is
> still
> > work to be done to ensure faithful rendition, but it's a start.
>
> Nice!
>
> Do you also have in mind of writing such files? That would very nicely
> implement an idea that no one ever got around too, of sharing "views"
> between PyMOL and Jmol...
>
>
A lofty goal. No such plans at this stage. Plenty to do just to get the
reading working. But I wouldn't rule it out. The problem, of course, would
be that a significant portion of what Jmol is capable of doing is not
representable in PyMOL. And, I'm sure, vice-versa, but that's not stopping
me from trying





> Egon
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> ___
> 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

<>--
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Make your web apps faster with AppDynamics
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Re: [Jmol-users] Problem with switching to JSMol

[Robert Hanson]

If you send me a copy of the page or a link to it, I can help you track
this down. Something simple, I'm sure.


On Fri, Feb 22, 2013 at 6:46 AM, Simone Sturniolo  wrote:

> Tried that. Every other order either increases the number of error
> messages, or leaves the situation unchanged.
>
>
> 2013/2/22 Paul Pillot 
>
>> Order matters in your js files links
>> I use the following declaration:
>> 
>> 
>>
>> That is with the minified version and without webGL.
>> Paul
>>
>> Le 22 févr. 2013 à 12:43, Simone Sturniolo a écrit :
>>
>> Hi,
>>
>> I'm trying to switch my JMol applet web page to JSMol - mainly to avoid
>> all the problems related with ever increasing restrictive security policies
>> for Java. I put all the main JSMol files in a folder, j2s in a subfolder,
>> loaded the scripts:
>>
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>>
>> completed the info section as follows:
>>
>> var main_info = {
>>  width: jmolW,
>>  height: jmolH,
>>  addSelectionOptions: false,
>>  color: "#00",
>>  debug: false,
>>  defaultModel: "",
>>  memoryLimit: 512,
>>  readyFunction: null,
>>  script: "",
>>  use: "HTML5",
>>  j2sPath: "jsmol/j2s",
>>  serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php";,
>>  console: "myJmol_infodiv",
>>  scriptCallback: "afterscript_callback",
>>  loadStructCallback: "afterload_callback",
>>  pickCallback: "pick_callback",
>>  src: null,
>> }
>>
>> left the rest of the code unchanged, basically following the instructions
>> found on http://wiki.jmol.org/index.php/JSmol, and now am running the
>> thing on Firefox 18.0.2. I get this error:
>>
>> TypeError: Jmol._getElement(...).style is undefined
>>
>> Jmol._getElement(this, "infotablediv").style.display = (tf ? "block" : 
>> "none");
>>
>> JSmol.js (line 395)
>>
>> What could be causing this, and what did I forget to do?
>> Thank you very much!
>>
>> Simone
>>
>>
>>
>> --
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Re: [Jmol-users] Jmol 13.1.13 released - several new features

[Robert Hanson]

On Fri, Feb 22, 2013 at 3:49 AM, Egon Willighagen <
egon.willigha...@gmail.com> wrote:

> On Fri, Feb 22, 2013 at 1:27 AM, Robert Hanson  wrote:
> > Most notably, Jmol 13.1.13 reads PyMOL session files (.PSE). There is
> still
> > work to be done to ensure faithful rendition, but it's a start.
>
> Nice!
>
> Do you also have in mind of writing such files? That would very nicely
> implement an idea that no one ever got around too, of sharing "views"
> between PyMOL and Jmol...
>
>
A lofty goal. No such plans at this stage. Plenty to do just to get the
reading working. But I wouldn't rule it out. The problem, of course, would
be that a significant portion of what Jmol is capable of doing is not
representable in PyMOL. And, I'm sure, vice-versa, but that's not stopping
me from trying





> Egon
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
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Chair, Chemistry Department
St. Olaf College
Northfield, MN
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Re: [Jmol-users] Problem with switching to JSMol

[Simone Sturniolo]

I know ^^, I sent another email right after that, sorry for the mistake!


2013/2/22 N David Brown 

> You didn't list the error :-)
>
>
> On 22 February 2013 15:07, Simone Sturniolo wrote:
>
>> Ok, the error message came up again, it's:
>>
>>
>>
>> 2013/2/22 Simone Sturniolo 
>>
>>> I used the new package and, as suggested, included only the JSmol.min.js
>>> script file. The result is a very similar error message, which now I can't
>>> manage to reproduce because Firefox keeps simply getting stuck when I try
>>> to load the page. I also lose all jQuery UI functionality that I had
>>> implemented, but this might be a cascade error, so I wouldn't pay much
>>> attention to it for now.
>>>
>>> Simone
>>>
>>>
>>>
>>>
>>> 2013/2/22 Angel Herráez 
>>>
 Ah, OK

 JSmol distribution is still not well roganized, I'm afraid. There's
 also a bit of confusion between Jmol-JSO and JSmol (which I'm
 planning to sort out and explain in the wiki)

 I suggest that you download from StOlaf. The link is in the wiki
 http://wiki.jmol.org/index.php/JSmol
 (there used to be a problem with capitalization, but I checked it is
 ok recently):
 http://chemapps.stolaf.edu/jmol/jsmol.zip

 That one is the latest development version and should contain
 JSmol.min.js
 If you still find problems, then for sure Bob will reply and deal
 with them.




 --
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 ___
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 https://lists.sourceforge.net/lists/listinfo/jmol-users

>>>
>>>
>>>
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>>
>>
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Re: [Jmol-users] Problem with switching to JSMol

[N David Brown]

You didn't list the error :-)

On 22 February 2013 15:07, Simone Sturniolo wrote:

> Ok, the error message came up again, it's:
>
>
>
> 2013/2/22 Simone Sturniolo 
>
>> I used the new package and, as suggested, included only the JSmol.min.js
>> script file. The result is a very similar error message, which now I can't
>> manage to reproduce because Firefox keeps simply getting stuck when I try
>> to load the page. I also lose all jQuery UI functionality that I had
>> implemented, but this might be a cascade error, so I wouldn't pay much
>> attention to it for now.
>>
>> Simone
>>
>>
>>
>>
>> 2013/2/22 Angel Herráez 
>>
>>> Ah, OK
>>>
>>> JSmol distribution is still not well roganized, I'm afraid. There's
>>> also a bit of confusion between Jmol-JSO and JSmol (which I'm
>>> planning to sort out and explain in the wiki)
>>>
>>> I suggest that you download from StOlaf. The link is in the wiki
>>> http://wiki.jmol.org/index.php/JSmol
>>> (there used to be a problem with capitalization, but I checked it is
>>> ok recently):
>>> http://chemapps.stolaf.edu/jmol/jsmol.zip
>>>
>>> That one is the latest development version and should contain
>>> JSmol.min.js
>>> If you still find problems, then for sure Bob will reply and deal
>>> with them.
>>>
>>>
>>>
>>>
>>> --
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_feb
>>> ___
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>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>
>>
>>
>> --
>> ___
>>
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>> simonesturni...@gmail.com
>>
>
>
>
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Re: [Jmol-users] Problem with switching to JSMol

[Simone Sturniolo]

Sorry, it seems like the mail was sent by mistake. The error message:

TypeError: b._getElement(...).style is undefined

...!c&&(this._isInfoVisible=c,this._infoObject?this._infoObject._showInfo(c):b._get...

JSmol.min.js (line 236)



2013/2/22 Simone Sturniolo 

> Ok, the error message came up again, it's:
>
>
>
> 2013/2/22 Simone Sturniolo 
>
>> I used the new package and, as suggested, included only the JSmol.min.js
>> script file. The result is a very similar error message, which now I can't
>> manage to reproduce because Firefox keeps simply getting stuck when I try
>> to load the page. I also lose all jQuery UI functionality that I had
>> implemented, but this might be a cascade error, so I wouldn't pay much
>> attention to it for now.
>>
>> Simone
>>
>>
>>
>>
>> 2013/2/22 Angel Herráez 
>>
>>> Ah, OK
>>>
>>> JSmol distribution is still not well roganized, I'm afraid. There's
>>> also a bit of confusion between Jmol-JSO and JSmol (which I'm
>>> planning to sort out and explain in the wiki)
>>>
>>> I suggest that you download from StOlaf. The link is in the wiki
>>> http://wiki.jmol.org/index.php/JSmol
>>> (there used to be a problem with capitalization, but I checked it is
>>> ok recently):
>>> http://chemapps.stolaf.edu/jmol/jsmol.zip
>>>
>>> That one is the latest development version and should contain
>>> JSmol.min.js
>>> If you still find problems, then for sure Bob will reply and deal
>>> with them.
>>>
>>>
>>>
>>>
>>> --
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_feb
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>
>>
>>
>> --
>> ___
>>
>> Nuovo indirizzo e-mail:
>> simonesturni...@gmail.com
>>
>
>
>
> --
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>
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Re: [Jmol-users] Problem with switching to JSMol

[Simone Sturniolo]

Ok, the error message came up again, it's:



2013/2/22 Simone Sturniolo 

> I used the new package and, as suggested, included only the JSmol.min.js
> script file. The result is a very similar error message, which now I can't
> manage to reproduce because Firefox keeps simply getting stuck when I try
> to load the page. I also lose all jQuery UI functionality that I had
> implemented, but this might be a cascade error, so I wouldn't pay much
> attention to it for now.
>
> Simone
>
>
>
>
> 2013/2/22 Angel Herráez 
>
>> Ah, OK
>>
>> JSmol distribution is still not well roganized, I'm afraid. There's
>> also a bit of confusion between Jmol-JSO and JSmol (which I'm
>> planning to sort out and explain in the wiki)
>>
>> I suggest that you download from StOlaf. The link is in the wiki
>> http://wiki.jmol.org/index.php/JSmol
>> (there used to be a problem with capitalization, but I checked it is
>> ok recently):
>> http://chemapps.stolaf.edu/jmol/jsmol.zip
>>
>> That one is the latest development version and should contain
>> JSmol.min.js
>> If you still find problems, then for sure Bob will reply and deal
>> with them.
>>
>>
>>
>>
>> --
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_feb
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>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
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>
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> simonesturni...@gmail.com
>



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Re: [Jmol-users] Problem with switching to JSMol

[Simone Sturniolo]

I used the new package and, as suggested, included only the JSmol.min.js
script file. The result is a very similar error message, which now I can't
manage to reproduce because Firefox keeps simply getting stuck when I try
to load the page. I also lose all jQuery UI functionality that I had
implemented, but this might be a cascade error, so I wouldn't pay much
attention to it for now.

Simone




2013/2/22 Angel Herráez 

> Ah, OK
>
> JSmol distribution is still not well roganized, I'm afraid. There's
> also a bit of confusion between Jmol-JSO and JSmol (which I'm
> planning to sort out and explain in the wiki)
>
> I suggest that you download from StOlaf. The link is in the wiki
> http://wiki.jmol.org/index.php/JSmol
> (there used to be a problem with capitalization, but I checked it is
> ok recently):
> http://chemapps.stolaf.edu/jmol/jsmol.zip
>
> That one is the latest development version and should contain
> JSmol.min.js
> If you still find problems, then for sure Bob will reply and deal
> with them.
>
>
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
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> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



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Re: [Jmol-users] Problem with switching to JSMol

[Angel Herráez]

Ah, OK

JSmol distribution is still not well roganized, I'm afraid. There's 
also a bit of confusion between Jmol-JSO and JSmol (which I'm 
planning to sort out and explain in the wiki)

I suggest that you download from StOlaf. The link is in the wiki 
http://wiki.jmol.org/index.php/JSmol
(there used to be a problem with capitalization, but I checked it is 
ok recently):
http://chemapps.stolaf.edu/jmol/jsmol.zip

That one is the latest development version and should contain 
JSmol.min.js
If you still find problems, then for sure Bob will reply and deal 
with them.



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Re: [Jmol-users] Problem with switching to JSMol

[Simone Sturniolo]

Hello Angel,

1) I downloaded the version found on sourceforge as linked on the wiki, and
I can't find JSmol.min.js, which I wanted to include at first

2) that could be the reason... I checked a few pages too though. I didn't
find any notable mistakes in my code, but of course, I might be wrong

3) it's not me who uses it, the function call is in JSmol.js.

Simone


2013/2/22 Angel Herráez 

> Hello Simone
>
> #1
> I believe (but am not sure) that with the latest versions you only
> need to call JSmol.min.js
> The call to j2sjmol.js will be done internally based on the path
> specufied in the Info variable.
>
> #2
> Information in the Wiki is not up-to-date (must find time to do it,
> and the WIki was blocked to edits until recently -- volunteers are
> welcome, by the way), so be careful.
> Check one of StOlaf's test/demo pages to see proper code.
>
> #3
> I'm not sure whether/how you can use  Jmol._getElement(...)
> Is that dcumented? I Don't see it and it may have changed.
>
>
>
>
> --
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Re: [Jmol-users] Problem with switching to JSMol

[Angel Herráez]

Hello Simone

#1
I believe (but am not sure) that with the latest versions you only 
need to call JSmol.min.js
The call to j2sjmol.js will be done internally based on the path 
specufied in the Info variable.

#2
Information in the Wiki is not up-to-date (must find time to do it, 
and the WIki was blocked to edits until recently -- volunteers are 
welcome, by the way), so be careful.
Check one of StOlaf's test/demo pages to see proper code.

#3
I'm not sure whether/how you can use  Jmol._getElement(...)
Is that dcumented? I Don't see it and it may have changed.



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Re: [Jmol-users] Problem with switching to JSMol

[Simone Sturniolo]

Tried that. Every other order either increases the number of error
messages, or leaves the situation unchanged.


2013/2/22 Paul Pillot 

> Order matters in your js files links
> I use the following declaration:
> 
> 
>
> That is with the minified version and without webGL.
> Paul
>
> Le 22 févr. 2013 à 12:43, Simone Sturniolo a écrit :
>
> Hi,
>
> I'm trying to switch my JMol applet web page to JSMol - mainly to avoid
> all the problems related with ever increasing restrictive security policies
> for Java. I put all the main JSMol files in a folder, j2s in a subfolder,
> loaded the scripts:
>
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>
> completed the info section as follows:
>
> var main_info = {
>  width: jmolW,
>  height: jmolH,
>  addSelectionOptions: false,
>  color: "#00",
>  debug: false,
>  defaultModel: "",
>  memoryLimit: 512,
>  readyFunction: null,
>  script: "",
>  use: "HTML5",
>  j2sPath: "jsmol/j2s",
>  serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php";,
>  console: "myJmol_infodiv",
>  scriptCallback: "afterscript_callback",
>  loadStructCallback: "afterload_callback",
>  pickCallback: "pick_callback",
>  src: null,
> }
>
> left the rest of the code unchanged, basically following the instructions
> found on http://wiki.jmol.org/index.php/JSmol, and now am running the
> thing on Firefox 18.0.2. I get this error:
>
> TypeError: Jmol._getElement(...).style is undefined
>
> Jmol._getElement(this, "infotablediv").style.display = (tf ? "block" : 
> "none");
>
> JSmol.js (line 395)
>
> What could be causing this, and what did I forget to do?
> Thank you very much!
>
> Simone
>
>
>
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Re: [Jmol-users] Problem with switching to JSMol

[Paul Pillot]

Order matters in your js files links
I use the following declaration:


That is with the minified version and without webGL.
Paul

Le 22 févr. 2013 à 12:43, Simone Sturniolo a écrit :

> Hi, 
> 
> I'm trying to switch my JMol applet web page to JSMol - mainly to avoid all 
> the problems related with ever increasing restrictive security policies for 
> Java. I put all the main JSMol files in a folder, j2s in a subfolder, loaded 
> the scripts:
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> completed the info section as follows:
> 
> var main_info = {
>  width: jmolW,
>  height: jmolH,
>  addSelectionOptions: false,
>  color: "#00",
>  debug: false,
>  defaultModel: "",
>  memoryLimit: 512,
>  readyFunction: null,
>  script: "",
>  use: "HTML5",
>  j2sPath: "jsmol/j2s",
>  serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php";,
>  console: "myJmol_infodiv",
>  scriptCallback: "afterscript_callback",
>  loadStructCallback: "afterload_callback",
>  pickCallback: "pick_callback",
>  src: null,
> }
> 
> left the rest of the code unchanged, basically following the instructions 
> found on http://wiki.jmol.org/index.php/JSmol, and now am running the thing 
> on Firefox 18.0.2. I get this error:
> 
> TypeError: Jmol._getElement(...).style is undefined
> Jmol._getElement(this, "infotablediv").style.display = (tf ? "block" : 
> "none");
> JSmol.js (line 395)
> 
> What could be causing this, and what did I forget to do?
> Thank you very much!
> 
> Simone
> 
> 
> -- 
> ___
> 
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> simonesturni...@gmail.com
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> Everyone hates slow websites. So do we.
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[Jmol-users] Problem with switching to JSMol

[Simone Sturniolo]

Hi,

I'm trying to switch my JMol applet web page to JSMol - mainly to avoid all
the problems related with ever increasing restrictive security policies for
Java. I put all the main JSMol files in a folder, j2s in a subfolder,
loaded the scripts:












completed the info section as follows:

var main_info = {
 width: jmolW,
 height: jmolH,
 addSelectionOptions: false,
 color: "#00",
 debug: false,
 defaultModel: "",
 memoryLimit: 512,
 readyFunction: null,
 script: "",
 use: "HTML5",
 j2sPath: "jsmol/j2s",
 serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php";,
 console: "myJmol_infodiv",
 scriptCallback: "afterscript_callback",
 loadStructCallback: "afterload_callback",
 pickCallback: "pick_callback",
 src: null,
}

left the rest of the code unchanged, basically following the instructions
found on http://wiki.jmol.org/index.php/JSmol, and now am running the thing
on Firefox 18.0.2. I get this error:

TypeError: Jmol._getElement(...).style is undefined

Jmol._getElement(this, "infotablediv").style.display = (tf ? "block" : "none");

JSmol.js (line 395)

What could be causing this, and what did I forget to do?
Thank you very much!

Simone



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Re: [Jmol-users] Jmol 13.1.13 released - several new features

[Egon Willighagen]

On Fri, Feb 22, 2013 at 1:27 AM, Robert Hanson  wrote:
> Most notably, Jmol 13.1.13 reads PyMOL session files (.PSE). There is still
> work to be done to ensure faithful rendition, but it's a start.

Nice!

Do you also have in mind of writing such files? That would very nicely
implement an idea that no one ever got around too, of sharing "views"
between PyMOL and Jmol...

Egon

-- 
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
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