Re: [Jmol-users] "Jmol" for iPads?

[Kevin Theisen]

Thanks for the tip Bob.

Yes, the access to caffeine.bonds.length would be done every time the loop 
repeats, which is very inefficient. The most inefficient part of Javascript is 
namespace calls, so when doing a.b.c, Javascript would have to find a, then 
find b, then find c. The reason this is inefficient is because Javascript 
scopes allow variables from all over. We stuck with the incrementing loop in 
tutorials for understandability, and also that those copy/pasting the code may 
have cases where order matters. But yes, the while(i--) loop removes the extra 
variable. I like this page that that goes over some Javascript tricks: 
http://www.sitepoint.com/google-closure-how-not-to-write-javascript/

I should note that optimizing Javascript can be tricky, as a technique that 
improves performance in one browser may actually reduce it in another.

Bests,
Kevin


On Apr 3, 2012, at 8:22 PM, Robert Hanson wrote:

> OK, I'm catching on. Just takes me a while. It still might be nice to develop 
> a general set of JavaScript functions that would be particularly handy. A 
> select() function would be very nice, for example. I guess that's what you 
> are doing
> 
> By the way, is this to prevent the repetitive access to 
> "caffeine.bonds.length" in JavaScript?
> 
>for(var i = 0, ii=caffeine.bonds.length; i 
> Is there a reason you do that? Is that a general problem that one should 
> avoid in JavaScript because of the interpreted nature of the language? If so, 
> this is simpler and cleaner:
> 
>   for(var i = caffeine.bonds.length; --i >= 0;)
> 
> Just something I learned along the way.
> 
> Bob
> 
> 
> 
> 
> On Tue, Apr 3, 2012 at 5:54 PM, Kevin Theisen  wrote:
> @Paul
> We do not currently have a querying function, and this is a great idea to 
> add. We have SMARTS support that we can pipe through, however, it will take 
> some work before we can deal with proteins in such a way. The script is 
> irrelevant to this functionality though, as the script in itself wouldn't 
> generate this ability.
> 
> @Bob
> Concerning the writing of a high level script on top of Javascript, I believe 
> it is redundant and produces unnecessary overhead. Chemists are quite smart, 
> and we have yet to encounter one that has been unable to use the ChemDoodle 
> API. Our goal is to make the API very clear and easy for chemists to master.
> 
> ChemDoodle components each have a VisualSpecifications object associated with 
> them that controls the rendering of graphics. As I linked before, you can use 
> this object to control how your graphics appear: 
> http://web.chemdoodle.com/tutorial/advanced/visual-specifications
> 
> "I think maybe it's limited to just a few simple operations being simple to 
> implement."
> 
> I'm not sure what you mean by this statement, are you trying to say we are 
> not capable of doing anything more complex? I assure you we have the 
> competence to do so, and the ChemDoodle API is adequately powerful.
> 
> Regardless, I believe both ChemDoodle and Jmol have weaknesses, and by 
> working together, we can help to achieve the functionality that everyone is 
> requesting. That is my goal. We continue to focus on expanding the ChemDoodle 
> Web Components, and I believe that the experience of the Jmol community will 
> help us to continue in the right direction. What Paul said also reinforced 
> what I stated before, there are many authors that use Jmol script, and I 
> think it's a better idea to try to write a Jmol script parser for ChemDoodle 
> rather than for us to go off and write our own. Personally, I would alway 
> choose the core Javascript interaction over a high level interface, but 
> certainly this type of parser would be very helpful for Jmol users.
> 
> Bests,
> Kevin
> 
> 
> 
> 
> On Apr 3, 2012, at 5:44 PM, Robert Hanson wrote:
> 
>> I wasn't necessarily trying to say anything. But I'm interested in what 
>> those controls can do. Is it limited to a few standard operations like 
>> changing overall rendering? I think maybe it's limited to just a few simple 
>> operations being simple to implement. At least now. For example, I haven't 
>> found a "select" command that lets me do something more interesting with a 
>> subset of the atoms. I could be missing it
>> 
>> On Tue, Apr 3, 2012 at 3:07 PM, Jeff Hansen  wrote:
>> I'm not with you Bob.  I checked the ChemDoodle demos (quite nice really) 
>> and I see the same kind of functionality as I see on many Jmol sites, radio 
>> buttons and such to control the appearance or behavior of a molecule.  Are 
>> you saying you think this is easier to create using Jmol scripting than it 
>> would be using Javascript?  I'm not sure I would agree with that.  It seems 
>> it is easier mostly because of the Jmol.js javascript library that hides 
>> much of the complexity.  Something similar could be done for the ChemDoodle 
>> approach I'm sure.  Or am I just missing something?
>> 
>> 
>> ***
>> J

Re: [Jmol-users] "Jmol" for iPads?

[Robert Hanson]

OK, I'm catching on. Just takes me a while. It still might be nice to
develop a general set of JavaScript functions that would be particularly
handy. A select() function would be very nice, for example. I guess that's
what you are doing

By the way, is this to prevent the repetitive access to
"caffeine.bonds.length" in JavaScript?

   for(var i = 0, ii=caffeine.bonds.length; i= 0;)

Just something I learned along the way.

Bob




On Tue, Apr 3, 2012 at 5:54 PM, Kevin Theisen  wrote:

> @Paul
> We do not currently have a querying function, and this is a great idea to
> add. We have SMARTS support that we can pipe through, however, it will take
> some work before we can deal with proteins in such a way. The script is
> irrelevant to this functionality though, as the script in itself wouldn't
> generate this ability.
>
> @Bob
> Concerning the writing of a high level script on top of Javascript, I
> believe it is redundant and produces unnecessary overhead. Chemists are
> quite smart, and we have yet to encounter one that has been unable to use
> the ChemDoodle API. Our goal is to make the API very clear and easy for
> chemists to master.
>
> ChemDoodle components each have a VisualSpecifications object associated
> with them that controls the rendering of graphics. As I linked before, you
> can use this object to control how your graphics appear:
> http://web.chemdoodle.com/tutorial/advanced/visual-specifications
>
> "I think maybe it's limited to just a few simple operations being simple
> to implement."
>
> I'm not sure what you mean by this statement, are you trying to say we are
> not capable of doing anything more complex? I assure you we have the
> competence to do so, and the ChemDoodle API is adequately powerful.
>
> Regardless, I believe both ChemDoodle and Jmol have weaknesses, and by
> working together, we can help to achieve the functionality that everyone is
> requesting. That is my goal. We continue to focus on expanding the
> ChemDoodle Web Components, and I believe that the experience of the Jmol
> community will help us to continue in the right direction. What Paul said
> also reinforced what I stated before, there are many authors that use Jmol
> script, and I think it's a better idea to try to write a Jmol script parser
> for ChemDoodle rather than for us to go off and write our own. Personally,
> I would alway choose the core Javascript interaction over a high level
> interface, but certainly this type of parser would be very helpful for Jmol
> users.
>
> Bests,
> Kevin
>
>
>
>
> On Apr 3, 2012, at 5:44 PM, Robert Hanson wrote:
>
> I wasn't necessarily trying to say anything. But I'm interested in what
> those controls can do. Is it limited to a few standard operations like
> changing overall rendering? I think maybe it's limited to just a few simple
> operations being simple to implement. At least now. For example, I haven't
> found a "select" command that lets me do something more interesting with a
> subset of the atoms. I could be missing it
>
> On Tue, Apr 3, 2012 at 3:07 PM, Jeff Hansen  wrote:
>
>> I'm not with you Bob.  I checked the ChemDoodle demos (quite nice really)
>> and I see the same kind of functionality as I see on many Jmol sites, radio
>> buttons and such to control the appearance or behavior of a molecule.  Are
>> you saying you think this is easier to create using Jmol scripting than it
>> would be using Javascript?  I'm not sure I would agree with that.  It seems
>> it is easier mostly because of the Jmol.js javascript library that hides
>> much of the complexity.  Something similar could be done for the ChemDoodle
>> approach I'm sure.  Or am I just missing something?
>>
>>
>>  ***
>> Jeff Hansen
>> Department of Chemistry and Biochemistry
>> DePauw University
>> 602 S. College Ave.
>> Greencastle, IN 46135
>> jhan...@depauw.edu
>> ***
>>
>>
>> On Apr 3, 2012, at 3:46 PM, Robert Hanson wrote:
>>
>> I think this question got lost in the lower reaches of my response. It's
>> fine if the answer is, "You can't do that, at least not yet."
>>
>> My point is that the power of Jmol isn't  the twiddle factor; it's the
>> scriptability (by people who are chemists, not JavaScript or Java experts).
>> I don't see any reason why one couldn't add a higher-level scripting
>> capability to ChemDoodle. Is the plan really to leave it at the JavaScript
>> level I see on those ChemDoodle web components pages?
>>
>> Bob
>>
>> On Mon, Apr 2, 2012 at 6:59 PM, Robert Hanson  wrote:
>>
>>>
>>>
>>>
>>> Say I have a page with a ChemDoodle version of caffeine.
>>>
>>> What do I do in ChemDoodle that would be equivalent to this in Jmol:
>>>
>>>   select {carbon}; color red
>>>
>>> or
>>>
>>>   rotate x 30
>>>
>>> or, I have a protein, let's say 1crn. What would I do in ChemDoodle to
>>> do this?
>>>
>>> select *; wireframe only
>>> select {helix}; cartoons only
>>>
>>> ? Those are pretty simple oper

Re: [Jmol-users] "Jmol" for iPads?

[Kevin Theisen]

@Paul
We do not currently have a querying function, and this is a great idea to add. 
We have SMARTS support that we can pipe through, however, it will take some 
work before we can deal with proteins in such a way. The script is irrelevant 
to this functionality though, as the script in itself wouldn't generate this 
ability.

@Bob
Concerning the writing of a high level script on top of Javascript, I believe 
it is redundant and produces unnecessary overhead. Chemists are quite smart, 
and we have yet to encounter one that has been unable to use the ChemDoodle 
API. Our goal is to make the API very clear and easy for chemists to master.

ChemDoodle components each have a VisualSpecifications object associated with 
them that controls the rendering of graphics. As I linked before, you can use 
this object to control how your graphics appear: 
http://web.chemdoodle.com/tutorial/advanced/visual-specifications

"I think maybe it's limited to just a few simple operations being simple to 
implement."

I'm not sure what you mean by this statement, are you trying to say we are not 
capable of doing anything more complex? I assure you we have the competence to 
do so, and the ChemDoodle API is adequately powerful.

Regardless, I believe both ChemDoodle and Jmol have weaknesses, and by working 
together, we can help to achieve the functionality that everyone is requesting. 
That is my goal. We continue to focus on expanding the ChemDoodle Web 
Components, and I believe that the experience of the Jmol community will help 
us to continue in the right direction. What Paul said also reinforced what I 
stated before, there are many authors that use Jmol script, and I think it's a 
better idea to try to write a Jmol script parser for ChemDoodle rather than for 
us to go off and write our own. Personally, I would alway choose the core 
Javascript interaction over a high level interface, but certainly this type of 
parser would be very helpful for Jmol users.

Bests,
Kevin




On Apr 3, 2012, at 5:44 PM, Robert Hanson wrote:

> I wasn't necessarily trying to say anything. But I'm interested in what those 
> controls can do. Is it limited to a few standard operations like changing 
> overall rendering? I think maybe it's limited to just a few simple operations 
> being simple to implement. At least now. For example, I haven't found a 
> "select" command that lets me do something more interesting with a subset of 
> the atoms. I could be missing it
> 
> On Tue, Apr 3, 2012 at 3:07 PM, Jeff Hansen  wrote:
> I'm not with you Bob.  I checked the ChemDoodle demos (quite nice really) and 
> I see the same kind of functionality as I see on many Jmol sites, radio 
> buttons and such to control the appearance or behavior of a molecule.  Are 
> you saying you think this is easier to create using Jmol scripting than it 
> would be using Javascript?  I'm not sure I would agree with that.  It seems 
> it is easier mostly because of the Jmol.js javascript library that hides much 
> of the complexity.  Something similar could be done for the ChemDoodle 
> approach I'm sure.  Or am I just missing something?
> 
> 
> ***
> Jeff Hansen
> Department of Chemistry and Biochemistry
> DePauw University
> 602 S. College Ave.
> Greencastle, IN 46135
> jhan...@depauw.edu
> ***
> 
> 
> On Apr 3, 2012, at 3:46 PM, Robert Hanson wrote:
> 
>> I think this question got lost in the lower reaches of my response. It's 
>> fine if the answer is, "You can't do that, at least not yet." 
>> 
>> My point is that the power of Jmol isn't  the twiddle factor; it's the 
>> scriptability (by people who are chemists, not JavaScript or Java experts). 
>> I don't see any reason why one couldn't add a higher-level scripting 
>> capability to ChemDoodle. Is the plan really to leave it at the JavaScript 
>> level I see on those ChemDoodle web components pages? 
>> 
>> Bob
>> 
>> On Mon, Apr 2, 2012 at 6:59 PM, Robert Hanson  wrote:
>> 
>> 
>> 
>> Say I have a page with a ChemDoodle version of caffeine.
>> 
>> What do I do in ChemDoodle that would be equivalent to this in Jmol:
>> 
>>   select {carbon}; color red
>> 
>> or
>> 
>>   rotate x 30
>> 
>> or, I have a protein, let's say 1crn. What would I do in ChemDoodle to do 
>> this?
>> 
>> select *; wireframe only
>> select {helix}; cartoons only
>> 
>> ? Those are pretty simple operations, of course. But I think they are 
>> representative of what I'm talking about. Are there any web pages out there 
>> using ChemDoodle that have simple scripting like this?
>> 
>> 
>> 
>> Bob
>> 
>> 
>> -- 
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>> 
>> 
>> 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
>>

Re: [Jmol-users] "Jmol" for iPads?

[Robert Hanson]

Charles, I got headless image generation going. The  current release of
Jmol, specifically JmolData.jar does it for PNG creation. There was a minor
snafu with JPG creation, so that will be in Jmol 12.2.20/12.3.20.

I can send you the PHP file I used if you want.

Bob

-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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
--
Better than sec? Nothing is better than sec when it comes to
monitoring Big Data applications. Try Boundary one-second 
resolution app monitoring today. Free.
http://p.sf.net/sfu/Boundary-dev2dev___
Jmol-users mailing list
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https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] "Jmol" for iPads?

[Robert Hanson]

I wasn't necessarily trying to say anything. But I'm interested in what
those controls can do. Is it limited to a few standard operations like
changing overall rendering? I think maybe it's limited to just a few simple
operations being simple to implement. At least now. For example, I haven't
found a "select" command that lets me do something more interesting with a
subset of the atoms. I could be missing it

On Tue, Apr 3, 2012 at 3:07 PM, Jeff Hansen  wrote:

> I'm not with you Bob.  I checked the ChemDoodle demos (quite nice really)
> and I see the same kind of functionality as I see on many Jmol sites, radio
> buttons and such to control the appearance or behavior of a molecule.  Are
> you saying you think this is easier to create using Jmol scripting than it
> would be using Javascript?  I'm not sure I would agree with that.  It seems
> it is easier mostly because of the Jmol.js javascript library that hides
> much of the complexity.  Something similar could be done for the ChemDoodle
> approach I'm sure.  Or am I just missing something?
>
>
> ***
> Jeff Hansen
> Department of Chemistry and Biochemistry
> DePauw University
> 602 S. College Ave.
> Greencastle, IN 46135
> jhan...@depauw.edu
> ***
>
>
> On Apr 3, 2012, at 3:46 PM, Robert Hanson wrote:
>
> I think this question got lost in the lower reaches of my response. It's
> fine if the answer is, "You can't do that, at least not yet."
>
> My point is that the power of Jmol isn't  the twiddle factor; it's the
> scriptability (by people who are chemists, not JavaScript or Java experts).
> I don't see any reason why one couldn't add a higher-level scripting
> capability to ChemDoodle. Is the plan really to leave it at the JavaScript
> level I see on those ChemDoodle web components pages?
>
> Bob
>
> On Mon, Apr 2, 2012 at 6:59 PM, Robert Hanson  wrote:
>
>>
>>
>>
>> Say I have a page with a ChemDoodle version of caffeine.
>>
>> What do I do in ChemDoodle that would be equivalent to this in Jmol:
>>
>>   select {carbon}; color red
>>
>> or
>>
>>   rotate x 30
>>
>> or, I have a protein, let's say 1crn. What would I do in ChemDoodle to do
>> this?
>>
>> select *; wireframe only
>> select {helix}; cartoons only
>>
>> ? Those are pretty simple operations, of course. But I think they are
>> representative of what I'm talking about. Are there any web pages out there
>> using ChemDoodle that have simple scripting like this?
>>
>>
>>
> Bob
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
> --
> Better than sec? Nothing is better than sec when it comes to
> monitoring Big Data applications. Try Boundary one-second
> resolution app monitoring today. Free.
>
> http://p.sf.net/sfu/Boundary-dev2dev___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> Better than sec? Nothing is better than sec when it comes to
> monitoring Big Data applications. Try Boundary one-second
> resolution app monitoring today. Free.
> http://p.sf.net/sfu/Boundary-dev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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
--
Better than sec? Nothing is better than sec when it comes to
monitoring Big Data applications. Try Boundary one-second 
resolution app monitoring today. Free.
http://p.sf.net/sfu/Boundary-dev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] "Jmol" for iPads?

[Paul Pillot]

@Jeff,
Jmol allows to control the display of specific parts of a model by an efficient 
query language inherited from Rasmol "Select hetero; do whatever; select 
protein; do whatever; ...".
To my use in class, this is a real motivation for using this software compared 
to a "twiddling" application.
In the web chemdoodle app specification, I came on this page : 
http://web.chemdoodle.com/tutorial/advanced/working-with-pdb-files
At the bottom it explains how you can change the display of proteins from the 
default cartoon. It does not appear to be as easy as a select process.
My understanding is that you can have access via javascript to core 
functionalities, but as Bob puts it, at the moment it involves a sensible 
amount of coding

I have delved into the chemdoodle code for an hybrid Jmol/chemdoodle sketcher 
project. It gave me the impression of being very well written and thus quite 
easily hackable. From my perspective, the best solution given all the amount of 
webpages using Jmol (and still even Chime !) would be to be able to control the 
display on the 3D canvas through a scripting language allowing selections and 
more.

Paul

Le 3 avr. 2012 à 22:07, Jeff Hansen a écrit :

> I'm not with you Bob.  I checked the ChemDoodle demos (quite nice really) and 
> I see the same kind of functionality as I see on many Jmol sites, radio 
> buttons and such to control the appearance or behavior of a molecule.  Are 
> you saying you think this is easier to create using Jmol scripting than it 
> would be using Javascript?  I'm not sure I would agree with that.  It seems 
> it is easier mostly because of the Jmol.js javascript library that hides much 
> of the complexity.  Something similar could be done for the ChemDoodle 
> approach I'm sure.  Or am I just missing something?
> 
> 
> ***
> Jeff Hansen
> Department of Chemistry and Biochemistry
> DePauw University
> 602 S. College Ave.
> Greencastle, IN 46135
> jhan...@depauw.edu
> ***
> 
> 
> On Apr 3, 2012, at 3:46 PM, Robert Hanson wrote:
> 
>> I think this question got lost in the lower reaches of my response. It's 
>> fine if the answer is, "You can't do that, at least not yet." 
>> 
>> My point is that the power of Jmol isn't  the twiddle factor; it's the 
>> scriptability (by people who are chemists, not JavaScript or Java experts). 
>> I don't see any reason why one couldn't add a higher-level scripting 
>> capability to ChemDoodle. Is the plan really to leave it at the JavaScript 
>> level I see on those ChemDoodle web components pages? 
>> 
>> Bob
>> 

--
Better than sec? Nothing is better than sec when it comes to
monitoring Big Data applications. Try Boundary one-second 
resolution app monitoring today. Free.
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Re: [Jmol-users] "Jmol" for iPads?

[Jeff Hansen]

I'm not with you Bob.  I checked the ChemDoodle demos (quite nice really) and I 
see the same kind of functionality as I see on many Jmol sites, radio buttons 
and such to control the appearance or behavior of a molecule.  Are you saying 
you think this is easier to create using Jmol scripting than it would be using 
Javascript?  I'm not sure I would agree with that.  It seems it is easier 
mostly because of the Jmol.js javascript library that hides much of the 
complexity.  Something similar could be done for the ChemDoodle approach I'm 
sure.  Or am I just missing something?


***
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***


On Apr 3, 2012, at 3:46 PM, Robert Hanson wrote:

> I think this question got lost in the lower reaches of my response. It's fine 
> if the answer is, "You can't do that, at least not yet." 
> 
> My point is that the power of Jmol isn't  the twiddle factor; it's the 
> scriptability (by people who are chemists, not JavaScript or Java experts). I 
> don't see any reason why one couldn't add a higher-level scripting capability 
> to ChemDoodle. Is the plan really to leave it at the JavaScript level I see 
> on those ChemDoodle web components pages? 
> 
> Bob
> 
> On Mon, Apr 2, 2012 at 6:59 PM, Robert Hanson  wrote:
> 
> 
> 
> Say I have a page with a ChemDoodle version of caffeine.
> 
> What do I do in ChemDoodle that would be equivalent to this in Jmol:
> 
>   select {carbon}; color red
> 
> or
> 
>   rotate x 30
> 
> or, I have a protein, let's say 1crn. What would I do in ChemDoodle to do 
> this?
> 
> select *; wireframe only
> select {helix}; cartoons only
> 
> ? Those are pretty simple operations, of course. But I think they are 
> representative of what I'm talking about. Are there any web pages out there 
> using ChemDoodle that have simple scripting like this?
> 
> 
> 
> Bob
> 
> 
> -- 
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
> 
> 
> 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
> --
> Better than sec? Nothing is better than sec when it comes to
> monitoring Big Data applications. Try Boundary one-second 
> resolution app monitoring today. Free.
> http://p.sf.net/sfu/Boundary-dev2dev___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

--
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monitoring Big Data applications. Try Boundary one-second 
resolution app monitoring today. Free.
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Re: [Jmol-users] "Jmol" for iPads?

[Robert Hanson]

I think this question got lost in the lower reaches of my response. It's
fine if the answer is, "You can't do that, at least not yet."

My point is that the power of Jmol isn't  the twiddle factor; it's the
scriptability (by people who are chemists, not JavaScript or Java experts).
I don't see any reason why one couldn't add a higher-level scripting
capability to ChemDoodle. Is the plan really to leave it at the JavaScript
level I see on those ChemDoodle web components pages?

Bob

On Mon, Apr 2, 2012 at 6:59 PM, Robert Hanson  wrote:

>
>
>
> Say I have a page with a ChemDoodle version of caffeine.
>
> What do I do in ChemDoodle that would be equivalent to this in Jmol:
>
>   select {carbon}; color red
>
> or
>
>   rotate x 30
>
> or, I have a protein, let's say 1crn. What would I do in ChemDoodle to do
> this?
>
> select *; wireframe only
> select {helix}; cartoons only
>
> ? Those are pretty simple operations, of course. But I think they are
> representative of what I'm talking about. Are there any web pages out there
> using ChemDoodle that have simple scripting like this?
>
>
>
Bob


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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] "Jmol" for iPads?

[Kevin Theisen]

> 
> I was thinking  that some simple format like 
> 
> write xxx.vrml

Thanks, I'll look into the Java API later today. Basically, I would like to 
call it via Java rather than the script. I will definitely have some questions 
for you, I'll send them offline.

> 
> ? Those are pretty simple operations, of course. But I think they are 
> representative of what I'm talking about. Are there any web pages out there 
> using ChemDoodle that have simple scripting like this?

I think we are saying the same thing. We don't have as many convenience actions 
as Jmol has, but we will be able to improve upon that as development continues. 
See the following pages for more information on manipulating the ChemDoodle Web 
Components:

http://web.chemdoodle.com/tutorial
http://web.chemdoodle.com/tutorial/input-events
http://web.chemdoodle.com/tutorial/animations
http://web.chemdoodle.com/tutorial/advanced/visual-specifications
http://web.chemdoodle.com/tutorial/advanced/working-with-pdb-files

-Kevin



On Apr 2, 2012, at 7:59 PM, Robert Hanson wrote:

> 
> 
> On Mon, Apr 2, 2012 at 3:20 PM, Kevin Theisen  wrote:
>> Marching cubes in JavaScript. Now there's a challenge! Kevin, I think if you 
>> want something like that, use JmolData.jar. That's headless and can run any 
>> script not involving image creation or font use. So creation of isosurfaces 
>> is fine. Jmol's marching cubes algorithm is highly efficient, now processing 
>> just about everything "progressively" meaning as a data stream, never 
>> actually creating a huge cube of data. It's possible exporting it as some 
>> other format would work.
> 
> 
> Exporting it to a format is not necessary. We just need to send Jmol atoms, 
> and then extract the vertices, normals and mesh connectivity of the surface. 
> That information will be ajaxed down as JSON, and immediately rendered. Is 
> this possible?
> 
> 
> I was thinking  that some simple format like 
> 
> write xxx.vrml
> 
> This is a very simple format that I would think would be easily parsed by 
> your JavaScript. It includes vertices, normals, and faces. 
> 
> Transform{children Transform{translation .449 -.189 .065
> children [
> Shape {
>  appearance  DEF _0 Appearance{material Material{diffuseColor 1 .648 0 
> transparency 0}} geometry IndexedFaceSet {
> coord Coordinate {
>point [
> 4.262 1.094 .447
> 4.262 1.068 .484
> 4.275 1.068 .447
> 4.262 1.2 .191
> 4.338 1.068 .191
> ...
> -5.071 -1.439 .702
> -5.087 -1.439 .447
> -5.033 -1.439 .191
>]
>   }
>   coordIndex [
> 2 0 1 -1
> 3 0 4 -1
> 4 0 2 -1
> ...
> 3988 4019 3990 -1
> 3990 4019 3982 -1
>   ]
>   solid FALSE
>   normalPerVertex TRUE
>normal Normal {
>   vector [
> .836 .456 .305
> .836 .539 .101
> .889 .43 .154
> ...
> 3150 3127 3125 -1
> 3125 3127 3127 -1
> 3127 3127 3119 -1
>   ]
>  }
> }
> 
> 
> 
>  
>> 
>> Kevin, could you tell us about some of your ideas for scriptability of 
>> ChemDoodle? I'm sure that's come a long way since I talked with you last.
> 
> I'm sure we will butt heads again on this, but this is a fundamental 
> difference between Jmol and ChemDoodle. Jmol's scripting system is necessary 
> because authors cannot manipulate Java at runtime, and therefore would have 
> no way to programmatically interact with Jmol. The ChemDoodle Web Components 
> library is pure Javascript, and can be manipulated in any way, at any time, 
> including runtime. So a script for the ChemDoodle Web Components is not 
> necessary, but that does not mean an author can't achieve the same behavior 
> in both environments.
> 
> 
> Ah, well, actually web developers have full access to the Viewer class, so 
> they can do anything with it they want, if they chose to. However, they would 
> never choose to.
>  
> > Does this make sense?
> 
> No, sorry, it still doesn't! :) I think I just need a "for instance":
> 
> I have a page with a ChemDoodle version of caffeine.
> 
> What do I do in ChemDoodle that would be equivalent to this in Jmol:
> 
>   select {carbon}; color red
> 
> or
> 
>   rotate x 30
> 
> or, I have a protein, let's say 1crn. What would I do in ChemDoodle to do 
> this?
> 
> select *; wireframe only
> select {helix}; cartoons only
> 
> ? Those are pretty simple operations, of course. But I think they are 
> representative of what I'm talking about. Are there any web pages out there 
> using ChemDoodle that have simple scripting like this?
> 
> 
> Bob
> 
> 
> -Kevin
> 
> 
> On Apr 2, 2012, at 2:31 PM, Robert Hanson wrote:
> 
>> 
>> 
>> On Mon, Apr 2, 2012 at 12:35 PM, Kevin Theisen  wrote:
>> I think these are all good points. In order to create a Jmol app for iPads, 
>> one would need to completely port the project to Objective-C, no easy task. 
>> To publish in Apple's App Store also costs money (99$/year), is very, very 
>> complicated and requires constant attention. And regardless of whether such 
>> an app would exist, Jmol authors would still need to "recreate" their 
>> content to work in these apps; the applets on thei

Re: [Jmol-users] "Jmol" for iPads?

[Robert Hanson]

On Mon, Apr 2, 2012 at 3:20 PM, Kevin Theisen  wrote:

> Marching cubes in JavaScript. Now there's a challenge! Kevin, I think if
> you want something like that, use JmolData.jar. That's headless and can run
> any script not involving image creation or font use. So creation of
> isosurfaces is fine. Jmol's marching cubes algorithm is highly efficient,
> now processing just about everything "progressively" meaning as a data
> stream, never actually creating a huge cube of data. It's possible
> exporting it as some other format would work.
>
>
> Exporting it to a format is not necessary. We just need to send Jmol
> atoms, and then extract the vertices, normals and mesh connectivity of the
> surface. That information will be ajaxed down as JSON, and immediately
> rendered. Is this possible?
>
>
I was thinking  that some simple format like

write xxx.vrml

This is a very simple format that I would think would be easily parsed by
your JavaScript. It includes vertices, normals, and faces.

Transform{children Transform{translation .449 -.189 .065
children [
Shape {
 appearance  DEF _0 Appearance{material Material{diffuseColor 1 .648 0
transparency 0}} geometry IndexedFaceSet {
coord Coordinate {
   point [
4.262 1.094 .447
4.262 1.068 .484
4.275 1.068 .447
4.262 1.2 .191
4.338 1.068 .191
...
-5.071 -1.439 .702
-5.087 -1.439 .447
-5.033 -1.439 .191
   ]
  }
  coordIndex [
2 0 1 -1
3 0 4 -1
4 0 2 -1
...
3988 4019 3990 -1
3990 4019 3982 -1
  ]
  solid FALSE
  normalPerVertex TRUE
   normal Normal {
  vector [
.836 .456 .305
.836 .539 .101
.889 .43 .154
...
3150 3127 3125 -1
3125 3127 3127 -1
3127 3127 3119 -1
  ]
 }
}





>
> Kevin, could you tell us about some of your ideas for scriptability of
> ChemDoodle? I'm sure that's come a long way since I talked with you last.
>
>
> I'm sure we will butt heads again on this, but this is a fundamental
> difference between Jmol and ChemDoodle. Jmol's scripting system is
> necessary because authors cannot manipulate Java at runtime, and therefore
> would have no way to programmatically interact with Jmol. The ChemDoodle
> Web Components library is pure Javascript, and can be manipulated in any
> way, at any time, including runtime. So a script for the ChemDoodle Web
> Components is not necessary, but that does not mean an author can't achieve
> the same behavior in both environments.
>
>
Ah, well, actually web developers have full access to the Viewer class, so
they can do anything with it they want, if they chose to. However, they
would never choose to.

> Does this make sense?

No, sorry, it still doesn't! :) I think I just need a "for instance":

I have a page with a ChemDoodle version of caffeine.

What do I do in ChemDoodle that would be equivalent to this in Jmol:

  select {carbon}; color red

or

  rotate x 30

or, I have a protein, let's say 1crn. What would I do in ChemDoodle to do
this?

select *; wireframe only
select {helix}; cartoons only

? Those are pretty simple operations, of course. But I think they are
representative of what I'm talking about. Are there any web pages out there
using ChemDoodle that have simple scripting like this?


Bob


> -Kevin
>
>
> On Apr 2, 2012, at 2:31 PM, Robert Hanson wrote:
>
>
>
> On Mon, Apr 2, 2012 at 12:35 PM, Kevin Theisen wrote:
>
>> I think these are all good points. In order to create a Jmol app for
>> iPads, one would need to completely port the project to Objective-C, no
>> easy task. To publish in Apple's App Store also costs money (99$/year), is
>> very, very complicated and requires constant attention. And regardless of
>> whether such an app would exist, Jmol authors would still need to
>> "recreate" their content to work in these apps; the applets on their
>> websites would still not work. So we are focusing on HTML5/WebGL as the
>> solution.
>>
>> Most of the performance issues with the ChemDoodle Web Components and
>> large proteins have been addressed, and the toolkit should never crash when
>> parsing any sized PDB file at this point. However, when using the backend
>> services, a PDB file may take a while to parse, and our Apache server
>> automatically terminates connections after 60 seconds, resulting in an
>> error. This is due to the fact that our Java backend is based on the
>> ChemDoodle desktop API, and therefore has overhead for working with the GUI
>> and for creating 2D graphics. We are currently in the process of separating
>> this logic out, so that really intensive functions become much more
>> efficient.
>>
>> I should note that our graphics are not limited to just proteins, the
>> ChemDoodle Web Components library handles small molecules, macromolecules,
>> crystals, spectra, and 2D as well as 3D (MOL/PDB/CIF/JCAMP/XYZ). We are
>> also working on surfaces (an experimental API is already included). Maybe
>> this is a good time to really push for an integration of Jmol functionality
>> on our backend though. We are still working on an efficient marching cubes
>> algorithm in Javascript, and unti

Re: [Jmol-users] "Jmol" for iPads?

[Kevin Theisen]

> Marching cubes in JavaScript. Now there's a challenge! Kevin, I think if you 
> want something like that, use JmolData.jar. That's headless and can run any 
> script not involving image creation or font use. So creation of isosurfaces 
> is fine. Jmol's marching cubes algorithm is highly efficient, now processing 
> just about everything "progressively" meaning as a data stream, never 
> actually creating a huge cube of data. It's possible exporting it as some 
> other format would work.


Exporting it to a format is not necessary. We just need to send Jmol atoms, and 
then extract the vertices, normals and mesh connectivity of the surface. That 
information will be ajaxed down as JSON, and immediately rendered. Is this 
possible?

> 
> Kevin, could you tell us about some of your ideas for scriptability of 
> ChemDoodle? I'm sure that's come a long way since I talked with you last.

I'm sure we will butt heads again on this, but this is a fundamental difference 
between Jmol and ChemDoodle. Jmol's scripting system is necessary because 
authors cannot manipulate Java at runtime, and therefore would have no way to 
programmatically interact with Jmol. The ChemDoodle Web Components library is 
pure Javascript, and can be manipulated in any way, at any time, including 
runtime. So a script for the ChemDoodle Web Components is not necessary, but 
that does not mean an author can't achieve the same behavior in both 
environments.

For instance, a Jmol script call would look like this:

jmol.runScript('actionA actionB');

While a ChemDoodle script would look like this:

component.actionA();
component.actionB();

It is actually more powerful in Javascript, because any aspect of the 
functionality may be tweaked this way (for instance, we can rename classes, 
create subclasses, add in our own functions), and does not require an explicit 
script language to be developed. Maybe the more pressing issue is the reuse of 
all the Jmol scripts. And maybe this is worth investigating, a Jmol script 
parser for ChemDoodle that will do the same actions. Does this make sense?

-Kevin


On Apr 2, 2012, at 2:31 PM, Robert Hanson wrote:

> 
> 
> On Mon, Apr 2, 2012 at 12:35 PM, Kevin Theisen  wrote:
> I think these are all good points. In order to create a Jmol app for iPads, 
> one would need to completely port the project to Objective-C, no easy task. 
> To publish in Apple's App Store also costs money (99$/year), is very, very 
> complicated and requires constant attention. And regardless of whether such 
> an app would exist, Jmol authors would still need to "recreate" their content 
> to work in these apps; the applets on their websites would still not work. So 
> we are focusing on HTML5/WebGL as the solution.
> 
> Most of the performance issues with the ChemDoodle Web Components and large 
> proteins have been addressed, and the toolkit should never crash when parsing 
> any sized PDB file at this point. However, when using the backend services, a 
> PDB file may take a while to parse, and our Apache server automatically 
> terminates connections after 60 seconds, resulting in an error. This is due 
> to the fact that our Java backend is based on the ChemDoodle desktop API, and 
> therefore has overhead for working with the GUI and for creating 2D graphics. 
> We are currently in the process of separating this logic out, so that really 
> intensive functions become much more efficient.
> 
> I should note that our graphics are not limited to just proteins, the 
> ChemDoodle Web Components library handles small molecules, macromolecules, 
> crystals, spectra, and 2D as well as 3D (MOL/PDB/CIF/JCAMP/XYZ). We are also 
> working on surfaces (an experimental API is already included). Maybe this is 
> a good time to really push for an integration of Jmol functionality on our 
> backend though. We are still working on an efficient marching cubes algorithm 
> in Javascript, and until that is complete, we could use Jmol instead. We 
> would just need to know how to call it and export the necessary information. 
> I think with your help, Bob, we could have this in a few days.
> 
> Marching cubes in JavaScript. Now there's a challenge! Kevin, I think if you 
> want something like that, use JmolData.jar. That's headless and can run any 
> script not involving image creation or font use. So creation of isosurfaces 
> is fine. Jmol's marching cubes algorithm is highly efficient, now processing 
> just about everything "progressively" meaning as a data stream, never 
> actually creating a huge cube of data. It's possible exporting it as some 
> other format would work.
> 
> Kevin, could you tell us about some of your ideas for scriptability of 
> ChemDoodle? I'm sure that's come a long way since I talked with you last.
> 
> -- 
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
> 
> 
> If nature does not answer first wha

Re: [Jmol-users] "Jmol" for iPads?

[Robert Hanson]

On Mon, Apr 2, 2012 at 12:35 PM, Kevin Theisen  wrote:

> I think these are all good points. In order to create a Jmol app for
> iPads, one would need to completely port the project to Objective-C, no
> easy task. To publish in Apple's App Store also costs money (99$/year), is
> very, very complicated and requires constant attention. And regardless of
> whether such an app would exist, Jmol authors would still need to
> "recreate" their content to work in these apps; the applets on their
> websites would still not work. So we are focusing on HTML5/WebGL as the
> solution.
>
> Most of the performance issues with the ChemDoodle Web Components and
> large proteins have been addressed, and the toolkit should never crash when
> parsing any sized PDB file at this point. However, when using the backend
> services, a PDB file may take a while to parse, and our Apache server
> automatically terminates connections after 60 seconds, resulting in an
> error. This is due to the fact that our Java backend is based on the
> ChemDoodle desktop API, and therefore has overhead for working with the GUI
> and for creating 2D graphics. We are currently in the process of separating
> this logic out, so that really intensive functions become much more
> efficient.
>
> I should note that our graphics are not limited to just proteins, the
> ChemDoodle Web Components library handles small molecules, macromolecules,
> crystals, spectra, and 2D as well as 3D (MOL/PDB/CIF/JCAMP/XYZ). We are
> also working on surfaces (an experimental API is already included). Maybe
> this is a good time to really push for an integration of Jmol functionality
> on our backend though. We are still working on an efficient marching cubes
> algorithm in Javascript, and until that is complete, we could use Jmol
> instead. We would just need to know how to call it and export the necessary
> information. I think with your help, Bob, we could have this in a few days.
>

Marching cubes in JavaScript. Now there's a challenge! Kevin, I think if
you want something like that, use JmolData.jar. That's headless and can run
any script not involving image creation or font use. So creation of
isosurfaces is fine. Jmol's marching cubes algorithm is highly efficient,
now processing just about everything "progressively" meaning as a data
stream, never actually creating a huge cube of data. It's possible
exporting it as some other format would work.

Kevin, could you tell us about some of your ideas for scriptability of
ChemDoodle? I'm sure that's come a long way since I talked with you last.

-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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] "Jmol" for iPads?

[Kevin Theisen]

I think these are all good points. In order to create a Jmol app for iPads, one 
would need to completely port the project to Objective-C, no easy task. To 
publish in Apple's App Store also costs money (99$/year), is very, very 
complicated and requires constant attention. And regardless of whether such an 
app would exist, Jmol authors would still need to "recreate" their content to 
work in these apps; the applets on their websites would still not work. So we 
are focusing on HTML5/WebGL as the solution.

Most of the performance issues with the ChemDoodle Web Components and large 
proteins have been addressed, and the toolkit should never crash when parsing 
any sized PDB file at this point. However, when using the backend services, a 
PDB file may take a while to parse, and our Apache server automatically 
terminates connections after 60 seconds, resulting in an error. This is due to 
the fact that our Java backend is based on the ChemDoodle desktop API, and 
therefore has overhead for working with the GUI and for creating 2D graphics. 
We are currently in the process of separating this logic out, so that really 
intensive functions become much more efficient.

I should note that our graphics are not limited to just proteins, the 
ChemDoodle Web Components library handles small molecules, macromolecules, 
crystals, spectra, and 2D as well as 3D (MOL/PDB/CIF/JCAMP/XYZ). We are also 
working on surfaces (an experimental API is already included). Maybe this is a 
good time to really push for an integration of Jmol functionality on our 
backend though. We are still working on an efficient marching cubes algorithm 
in Javascript, and until that is complete, we could use Jmol instead. We would 
just need to know how to call it and export the necessary information. I think 
with your help, Bob, we could have this in a few days.

So hopefully, as the project develops, it will become an easy procedure to 
substitute ChemDoodle for Jmol as the frontend on platforms that don't support 
Java. Certainly, we are doing our best to work towards that goal. As with all 
things, support matters, so if anyone is interested in seeing this project 
succeed, please help us by giving us suggestions and advice and by mentioning 
the open source ChemDoodle Web Components to your colleagues and students.

On an aside, we are working with eTextbook vendors, so our technologies will be 
accessible to authors on a number of platforms. So working with us is a good 
way to get the functionality you want on the devices that you want.

-Kevin






On Apr 2, 2012, at 11:37 AM, Robert Hanson wrote:

> OK, there are really three threads here:
> 
> 1) Jmol app for the iPad
> 2) Jmol export of iPad-ready model twiddles that can be embedded in iBooks
> 3) Jmol applet-equivalent for browsers running in Java-challenged platforms
> 
> (1) was the discussion I was starting. But now I think that's off track. I 
> guess I don't know if anyone really is interested in that.
> 
> (2) is easy. Otis showed how that is possible, and we could make it simpler. 
> A Collada exporter is somewhere on my TODO list.
> 
> Craig, if I hear what you are saying, you're not so much interested in (1) or 
> (2). You are interested in a browser-based scriptable applet, (3). 
> ChemDoodle's experiment  is ongoing, and so far it is proving  to be 
> marginally effective, as far as I can tell. It is a hybrid of (2) and (3) -- 
> a relatively unscriptable twiddlable model for the browser (with interesting 
> metainformation available from a server). 
> 
> Regarding (3), I'd need to see real-time molecular surface creation, 
> calculation of MOs from wave functions, decent translucency, and effective 
> graphical manipulation of large systems before I would endorse HTML5 as the 
> way to go in general. So I'm hoping the ChemDoodle experiment will continue 
> and we will hear more good stuff from them. The idea of porting 7 Mb of Java 
> code to interpreted JavaScript source, however, is mind numbing. That's just 
> asking for the impossible, I think, in terms of practical performance. (Of 
> course, people said that about Jmol being written in Java, as well...) I'm 
> very interested in hearing more about the practical limitations of HTML5. I 
> don't know why ChemDoodle was crashing with simple rendering of large 
> proteins last time I tried it (last summer, I think), but I will remind those 
> reading this that there is a reason Jmol works so well, and it is mostly 
> because we do NOT use standard graphical toolkits.
> 
> Is that more to the point?
> 
> -- 
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College


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Re: [Jmol-users] "Jmol" for iPads?

[Robert Hanson]

OK, there are really three threads here:

1) Jmol app for the iPad
2) Jmol export of iPad-ready model twiddles that can be embedded in iBooks
3) Jmol applet-equivalent for browsers running in Java-challenged platforms

(1) was the discussion I was starting. But now I think that's off track. I
guess I don't know if anyone really is interested in that.

(2) is easy. Otis showed how that is possible, and we could make it
simpler. A Collada exporter is somewhere on my TODO list.

Craig, if I hear what you are saying, you're not so much interested in (1)
or (2). You are interested in a browser-based scriptable applet, (3).
ChemDoodle's experiment  is ongoing, and so far it is proving  to be
marginally effective, as far as I can tell. It is a hybrid of (2) and (3)
-- a relatively unscriptable twiddlable model for the browser (with
interesting metainformation available from a server).

Regarding (3), I'd need to see real-time molecular surface creation,
calculation of MOs from wave functions, decent translucency, and effective
graphical manipulation of large systems before I would endorse HTML5 as the
way to go in general. So I'm hoping the ChemDoodle experiment will continue
and we will hear more good stuff from them. The idea of porting 7 Mb of
Java code to interpreted JavaScript source, however, is mind numbing.
That's just asking for the impossible, I think, in terms of practical
performance. (Of course, people said that about Jmol being written in Java,
as well...) I'm very interested in hearing more about the practical
limitations of HTML5. I don't know why ChemDoodle was crashing with simple
rendering of large proteins last time I tried it (last summer, I think),
but I will remind those reading this that there is a reason Jmol works so
well, and it is mostly because we do NOT use standard graphical toolkits.

Is that more to the point?

-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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] "Jmol" for iPads?

[Craig T Martin]

Looking at my comment below out of context, I feel a need to clarify. I am 
EXTREMELY thankful to the dedicated core who have put so much into the 
development of Jmol. I have benefitted greatly from the selfless efforts of 
others.  I am also very aware that my request to move Jmol away from Java and 
to HTML5/OpenGL is not at all trivial. If no one wants to take this on, I will 
fully understand, and I regret that I do not have the skills to take this on 
myself. So please don't take this as a demand, but rather as a 
request/suggestion... As a user, I see this as the next big challenge for Jmol, 
but I appreciate that it is both big and a challenge.

Craig Martin

> Message: 2
> Date: Fri, 30 Mar 2012 08:53:35 -0500
> From: Robert Hanson 
> Subject: Re: [Jmol-users] "Jmol" for iPads?
> 
> Absolutely.
> 
> On Fri, Mar 30, 2012 at 8:01 AM, Craig T Martin wrote:
> 
>> The challenge of open source is "who's going to fix this and how?" Perhaps
>> our discussion should move in that direction?
>> 
> -- 
> Robert M. Hanson
> Professor of Chemistry


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Re: [Jmol-users] "Jmol" for iPads?

[Robert Hanson]

Jmol has, in fact, been factored into all of these areas. That was the
Android project. So all Jmol is entirely independent of platform except for
calls to a specific "platform" class that inserts whatever
platform-specific aspects are required, such as images, fonts, and
graphics.

So that's not the issue.

Obviously we're not talking here about the applet -- the applet is out.
Period. You won't be building web pages around Jmol and doing something
with them on the iPad. We aren't talking about adding Jmol to a browser
viewing Proteopedia, for example. We aren't talking about building links
around the applet that script it. (That could be done in Android, but I
think probably not on the iPad.)  You won't be customizing Jmol to do some
specific task -- unless of course you are an iPad developer yourself and
are embedding all this in your specific app. So let's not go there. That's
way more involved.

What we are talking about is a Jmol App. Independent, isolated (like all
iPad apps), stand-alone. The real question, in my mind, is this:

What is it about a Jmol app that would justify the effort put into creating
it?

Questions for discussion:

Q: If you had a Jmol app on the iPad, what would you do want to do with it?

Q: How would you envision getting models into it?

Q: What new features would you want implemented that incorporate into the
app features of the iPad that are not available on the non-tablet
platforms? For example, would you have gestures, and if so, what gestures?
Would you use the gyro? (These features are already in Jmol, but are there
other features of the iPad that are unique to it that you would want to
utilize?)

Q: What features of Jmol would you remove to fit the restricted input
characteristics of the iPad? For example, What would you use to replace the
pop-up menu? How would you activate and navigate that? How would  you
handle the much lower resolution of a "touch" than a mouse click? How would
you handle the single action of "mouse down/up" rather than
single/double-click/left/right/ctrl/alt options?

I think these are the real issues. A Jmol app for the iPad is not simply a
port to another system. It's a totally different interface that could
incorporate android-like capabilities of the iPad (gestures, gyro, which
are already in Jmol) and perhaps special features of the iPad not in
android, if those exist, but also would have to be reduced to the strict
limitations of the iPad input mechanisms and Apple app-isolation rules.

Bob


On Fri, Mar 30, 2012 at 5:50 PM, Charles Harrison Shubert
wrote:

>  Maybe the first question is "what needs to be fixed?"
>
>  Let's assume for the sake of discussion that there is a port of Jmol to
> iPads to address the need for image updating performance.  Let's also
> assume that Jmol has been factored into UI, scripting, parsing raw source,
> image calculation, and image rendering components (or libraries) that can
> be worked on separately.
>
>  What pieces of the existing Jmol code base would go into each of these
> iPad components?  How would they need to be changed to run on an iPad?
>
>  --Chuck
>
>  On Mar 30, 2012, at 9:53 AM, Robert Hanson wrote:
>
> Absolutely.
>
> On Fri, Mar 30, 2012 at 8:01 AM, Craig T Martin wrote:
>
>> The challenge of open source is "who's going to fix this and how?"
>> Perhaps our discussion should move in that direction?
>>
>>
>>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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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phone: 507-786-3107


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Re: [Jmol-users] "Jmol" for iPads?

[Charles Harrison Shubert]

Maybe the first question is "what needs to be fixed?"

Let's assume for the sake of discussion that there is a port of Jmol to iPads 
to address the need for image updating performance.  Let's also assume that 
Jmol has been factored into UI, scripting, parsing raw source, image 
calculation, and image rendering components (or libraries) that can be worked 
on separately.

What pieces of the existing Jmol code base would go into each of these iPad 
components?  How would they need to be changed to run on an iPad?

--Chuck

On Mar 30, 2012, at 9:53 AM, Robert Hanson wrote:

Absolutely.

On Fri, Mar 30, 2012 at 8:01 AM, Craig T Martin 
mailto:cmar...@chem.umass.edu>> wrote:
The challenge of open source is "who's going to fix this and how?" Perhaps our 
discussion should move in that direction?



--
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St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

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Re: [Jmol-users] "Jmol" for iPads?

[Robert Hanson]

Absolutely.

On Fri, Mar 30, 2012 at 8:01 AM, Craig T Martin wrote:

> The challenge of open source is "who's going to fix this and how?" Perhaps
> our discussion should move in that direction?
>
>
>
-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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] "Jmol" for iPads?

[Craig T Martin]

Wow. I've stepped into (and probably added fuel to) a firestorm.

I'd like to suggest that this is not the forum for arguing the merits of iOS vs 
Android. Some of us are a bit fanatical about iOS (OK, I'm one of them), and 
some fanatical about Android. But we're all unified in being fanatical about 
Jmol.

I think we can all agree that Jmol should be accessible to as many people on as 
many platforms as possible. In the days of CHIME, one could write a WEB page 
that included glorious interactive content, but users who did not install the 
plug-in (or who were using newer cutting edge browsers, if I remember 
correctly) were met with an error message. Jmol's biggest advancement (among a 
huge list of advancements) was fixing that glaring problem. I can write a WEB 
page with embedded molecules and be assured that every user sees what I want.

Alas, we're now revisiting history. One can argue that this is all Apple's 
fault for not supporting Java, but that won't change reality. We can't simply 
tell users the equivalent of "well, just stay with Netscape 4.x and everything 
will be fine." They will use what they use - and we want to reach them all. And 
as with CHIME, authors will be less inclined to use Jmol if they know that 
there are significant markets that cannot be reached.

So yes, Jmol should run on Android, and yes, it should run on iOS, regardless 
of where one stands in the platform war... The challenge of open source is 
"who's going to fix this and how?" Perhaps our discussion should move in that 
direction?

Thanks to everyone for their passions - that's what keeps Jmol dynamic!!

Craig Martin
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Re: [Jmol-users] "Jmol" for iPads?

[Egon Willighagen]

All,

On Fri, Mar 30, 2012 at 10:29 AM, Egon Willighagen
 wrote:
> I find it very disturbing that educators are even considering creating
> a learning environment where students are restricted in their
> learning! That is just another step back to the middle ages... Henry,
> I very much appreciate that people use the platform on which they can
> perform their work most efficient; do not disallow your students the
> same choice!

I like to clarify this point a bit. In was partly in reply to the
email from Henry, but also to other emails in this thread.

What I observe at many universities is plans where the university has
beautiful plans how they like to teach students. This can be a choice
for using iPad to show students protein structures, as outed in the
email thread. We have seen this for a long time: we select one
pedagogical book for a topic. However, that one book may not align
best with how all students learn; probably it will with the majority,
but not all.

Maastricht University expects students to decide themselves which book
to pick, and we here offer them two or three options. However, this
has as downside that they can only read them at the university, as we
do not provide those books for free, nor expect them to buy them
(which they would not be able to, anyway).

Here, the educational institute 'knows best' how the students will
learn. However, all students have their own way of learning. Some
prefer learning basic facts by heart, others prefer understanding and
apply systems later. Similarly, there are various ways to explain
something. Pure mathematics, visual explanation, explanation by
example. Books prefer solutions. But who are we to decide what is
best? Should we keep acting like a church that describes what is best
for the flock?

That is where my clumsy referral to the middle ages come from: an
institute that decides what it best, leaving no option for
alternatives. I should have phrased it like that.

My apologies that the email reads like a flamebait; I am strong about
teaching students to think for themselves, which requires giving them
room to make choices for themselves; I was overenthusiastic about it.

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
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Re: [Jmol-users] "Jmol" for iPads?

[Egon Willighagen]

Dear Henry,

On Fri, Mar 30, 2012 at 11:01 AM, Rzepa, Henry S  wrote:
>> I find it very disturbing that educators are even considering creating
>> a learning environment where students are restricted in their
>> learning! That is just another step back to the middle ages... Henry,
>> I very much appreciate that people use the platform on which they can
>> perform their work most efficient; do not disallow your students the
>> same choice!
>
> I a not sure I understand what you are saying Egon. If there is eg no Jmol on 
> e.g. an  iPad or Kindle, is that extending choice?

It most certainly is not... I would love to see Jmol work on the iPad
or Kindle...

> It could be viewed as a lack of choice, ie  if you want the features of Jmol 
> on a mobile device, your choice is currently restricted just to  Android.

'just' :)

> I mentioned in my post standards, ie epub2, epub3.  There are widely 
> available readers for these on all platforms (well, not yet epub3, but it 
> will come). Again,  I am not sure where the lack of choice there is?

I am wondering if these will allow the interactivity we want as done
in Proteopedia. Will those formats be an electronic dead tree, or
proper HTML with embedding of interactive things (applet/WebGL/...)
which can be interacted with?

> WebGL is expected shortly on both types, again no lack of choice.

My argument was not against WebGL, but against iPad, and in reply to
your 8 points in comparing iPad to Android...

The interaction and accessibility is crucial... we want students to
not just look at a protein, but indeed also to allow them do things
the material did not immediately envision, like the downloading of
that structure into other tools...

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
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Re: [Jmol-users] "Jmol" for iPads?

[Rzepa, Henry S]

> 
> I find it very disturbing that educators are even considering creating
> a learning environment where students are restricted in their
> learning! That is just another step back to the middle ages... Henry,
> I very much appreciate that people use the platform on which they can
> perform their work most efficient; do not disallow your students the
> same choice!
> 
I a not sure  I understand what you are saying Egon.   If there is eg no  Jmol 
on e.g. an  iPad or Kindle , is that  extending choice?  It could be viewed as 
a lack of choice, ie  if you want the features of Jmol on a mobile device, your 
choice is  currently restricted just to  Android.

I mentioned in my post standards, ie epub2, epub3.  There are widely available 
readers for these on all platforms (well, not yet epub3, but it will come).   
Again,  I am not sure where the lack of choice there is? WebGL is expected 
shortly on both types, again no lack of choice.   Solutions based on e.g. 
HTML5/WebGL would run on both platforms, offering choice. My post was meant to 
outline options, and according to your priorities you would be free to make 
your choice.   My own teaching notes are actually available for all three types 
of tablet, as well as all desktop browsers. 

Where  I do worry is if the choice you have is restricted by the publishers of 
the software.  Thus, no access to the data underlying the program  (because it 
is sandboxed, or held on a server)  is in my opinion a very serious  lack of 
choice, restricting the options the student has.  This lack of choice is what 
we have to guard against. 


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Re: [Jmol-users] "Jmol" for iPads?

[Egon Willighagen]

On Thu, Mar 29, 2012 at 3:08 PM, Rzepa, Henry S  wrote:
> 1. Do you want a QA controlled (by Apple) environment,  or  the more 
> advertising-oriented environment of Android?

I do have several Android apps installed without advertisement... I do
not think the above choice is accurate...

> 2. Which app store best contains the kind of apps that you want?

Here too, you have way more choice with Android: e.g. there is
F-Droid, an app store dedicated to open source apps:

http://f-droid.org/

(Bob, maybe you could upload the Jmol app there too?)

> 4. Security, again allegedly, is lower on Android.

F-Droid has interesting apps in this area...

> 5. iPad is not fragmented,  but  Android is device fragmented (unless of 
> course you consider  Samsung as the only alternative player).

Choice == fragmentation. Do you want a monopoly (no fragmentation) or
a choice (fragmentation)... if you rather pay a lot for not having to
make choices, then iPad is your thing. If you like to encourage your
students to explore things no one has done before, then iPad/Android
is even be a choice.

> 6. Few Android devices update the OS as often as  Apple does IOS.

Android's can be installed with custom ROMs which you can update any
time of the day you like.

Forcing your students to use certain hardware and certain software may
sound cool, but ask a student and ask him/her why she cannot as study
as optimal as he/she would like... you'll hear one thing: access to
study material. So, if you go iPad, make sure that all students has
iPads 24/7 and can install/view and study whatever educational
material they deem needed...

I find it very disturbing that educators are even considering creating
a learning environment where students are restricted in their
learning! That is just another step back to the middle ages... Henry,
I very much appreciate that people use the platform on which they can
perform their work most efficient; do not disallow your students the
same choice!

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

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Re: [Jmol-users] "Jmol" for iPads?

[Jonathan Gutow]

Uh..Oh...Now I'm embarrassed...this was workingI apologize to anybody who 
tried this.  The server side generation of images seems to be broken again.  I 
hope to have time to chase this over the weekend.  However, this means one more 
problem has been found and can be rectified. I will post again, when there is 
something working for people to try...

Jonathan
On Mar 29, 2012, at 4:39 PM, jmol-users-requ...@lists.sourceforge.net wrote:

> Presently, I'm working on this for the python scripted server that supports 
> the Web interface for the SageMath Package (www.sagemath.org).  
> 
> If you want to see a server running this experimental technology, visit my 
> test server at  
> http://141.233.196.149:
> Login as: testJmol with a password of: test.
> This is a very wimpy old computer I keep running for test purposes.  Don't 
> expect very fast responses.  Anyway, if you click on any of the 
> pages/worksheets listed after you log in, you should see pages that use Jmol 
> to display 3-D objects.  The displays initially are static .png images 
> generated by JmolData.jar running on the server.  Jmol only becomes live when 
> you click on the "make interactive" button.
> 
> So the way to do this is generate system calls from your scripting engine 
> like this:
> 
> java -jar "path to JmolData.jar" -iox -s "path to script that loads molecule 
> and sets view" -J "write 'filename.png'"
> 
> Jonathan

 Dr. Jonathan H. Gutow
Chemistry Departmentgu...@uwosh.edu
UW-Oshkosh  Office: 920-424-1326
800 Algoma BoulevardFAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow

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Re: [Jmol-users] "Jmol" for iPads?

[Gutow, Jonathan H]

Chuck,

As Bob said, latest version means literally the bleeding edge releases 12.2.19 
and 12.3.19.  I had been using the full-fledged Jmol on as server to generate 
images and realized that I could lose the server-side GUI if we could figure 
out how to generate images using a GUI free version of Jmol.  JmolData.jar was 
set up that way for extracting data from molecule files.  When I asked Bob 
about including image file generation he attacked the problem with his usual 
vigor.  Now script commands like "write PNG 'filename.png'" passed to 
JmolData.jar will write a png file of the view specified by the script even if 
the server does not have a GUI running.

Presently, I'm working on this for the python scripted server that supports the 
Web interface for the SageMath Package (www.sagemath.org).  

If you want to see a server running this experimental technology, visit my test 
server at  
http://141.233.196.149:
Login as: testJmol with a password of: test.
This is a very wimpy old computer I keep running for test purposes.  Don't 
expect very fast responses.  Anyway, if you click on any of the 
pages/worksheets listed after you log in, you should see pages that use Jmol to 
display 3-D objects.  The displays initially are static .png images generated 
by JmolData.jar running on the server.  Jmol only becomes live when you click 
on the "make interactive" button.

So the way to do this is generate system calls from your scripting engine like 
this:

java -jar "path to JmolData.jar" -iox -s "path to script that loads molecule 
and sets view" -J "write 'filename.png'"

Jonathan


On Mar 29, 2012, at 10:07 AM, Charles Harrison Shubert wrote:

> Hi Johathan,
> 
> Could you say more about what "latest version" means, how to run JmolData.jar 
> headless on the server, and  how it works as an image generator?  This might 
> be a very nice way for me to get the iPad functionality I'm looking for.
> 
> Thanks,
> 
> --Chuck
> 
> On Mar 29, 2012, at 10:08 AM, Gutow, Jonathan H wrote:
> 
>> The latest version of JmolData.jar can be run headless on the server to 
>> generate image files.

Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh   Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow/


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Re: [Jmol-users] "Jmol" for iPads?

[Robert Hanson]

I'll  let Jonathan explain JmolData. "latest version" means in this context
12.2.19 or 12.3.19, which I've scheduled for imminent release. We just
recently realized that one could  produce images within this headless mode,
so that's why you need the latest version, whether it is 12.2 or 12.3.

On Thu, Mar 29, 2012 at 10:07 AM, Charles Harrison Shubert  wrote:

> Hi Johathan,
>
> Could you say more about what "latest version" means, how to run
> JmolData.jar headless on the server, and  how it works as an image
> generator?  This might be a very nice way for me to get the iPad
> functionality I'm looking for.
>
> Thanks,
>
> --Chuck
>
> On Mar 29, 2012, at 10:08 AM, Gutow, Jonathan H wrote:
>
> > The latest version of JmolData.jar can be run headless on the server to
> generate image files.
>
>
>
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Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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] "Jmol" for iPads?

[Charles Harrison Shubert]

Hi Johathan,

Could you say more about what "latest version" means, how to run JmolData.jar 
headless on the server, and  how it works as an image generator?  This might be 
a very nice way for me to get the iPad functionality I'm looking for.

Thanks,

--Chuck

On Mar 29, 2012, at 10:08 AM, Gutow, Jonathan H wrote:

> The latest version of JmolData.jar can be run headless on the server to 
> generate image files.


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Re: [Jmol-users] "Jmol" for iPads?

[Otis Rothenberger]

I'm saddened by the fact that for the foreseeable future this is dragging us 
back to the "see the pretty molecule spin" age. In the cases where this is 
useful (pretty molecules spinning), I agree with Jonathan that there are 
textbook like presentation options. I would add to Jonathan's suggestions a 
reminder that Jmol to Collada is now pretty easy via AccuTrans 3D. There is 
even a batch translation process which works at lightning speed. The Collada 
files open directly in Mac's Preview in manipulatable form. They also import 
into iBook Author producing a manipulatable model for iPad.

This use of AccuTrans 3D is MUCH better than the more convoluted approach I 
posted previously.

Otis

--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com


> 
> 
> a) For fixed textbook like presentations, views can be packaged as .pngs or 
> animated .gifs (to show spinning).  In many cases Jmol content consists of 
> views that change with the click of a button in a known way (this is not the 
> case for servers that open different data files at user request...see (b)).  
> I could envision modifying my Export-to-Web code so that it would generate a 
> static .png and a spinning .gif of each view.  Rather than putting Jmol in 
> the page when the user clicks a button these images would be put in the page 
> with a button to click to "make interactive".  If the OS does not support 
> JavaVMs the user would get a simple dialog message.
> 

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Re: [Jmol-users] "Jmol" for iPads?

[Gutow, Jonathan H]

My family has an Ipad we use extensively.  However, I mostly agree with Bob.  
The Ipad/Tablet devices are good for consuming information created by others.  
Thus I do think they will make significant inroads in the book market.  
However, the fact that the Ipad makes it difficult to consume certain kinds of 
web-based content is likely to be a problem long term.  Here's how I see it:

1) Why Apple has migrated to the IOS environment.  The original MacOS was very 
tightly controlled (as is IOS) and was relatively easy for Apple to figure out 
how to provide a seamless and glitzy (for the time) user experience.  
Eventually, this closed system became a problem and Apple's market share began 
to decline.  That is when OSX was released.  Because OSX was based on an open 
BSD Unix users suddenly had access to all the richness of the more open 
markets.  I believe this temporarily saved the Macintosh.  However, the growing 
success of the open-source movement and the growing maturity of various flavors 
of LINUX Desktop environments is impacting the market for closed source desktop 
and server OSes.  I think Apple and other companies that sell closed-source 
OSes are expecting to make less and less money on their desktop and server 
OSes.  They are shifting towards the tablet market.  Apple is entering the 
market in the same way it entered the PC market.  Eventually, I suspect they 
will have to shift towards supporting a broader spectrum of technology and 
software if their competitors and open source options do, just as they did with 
the MacOS.

2) I see two initial options for Jmol usage:
a) For fixed textbook like presentations, views can be packaged as .pngs or 
animated .gifs (to show spinning).  In many cases Jmol content consists of 
views that change with the click of a button in a known way (this is not the 
case for servers that open different data files at user request...see (b)).  I 
could envision modifying my Export-to-Web code so that it would generate a 
static .png and a spinning .gif of each view.  Rather than putting Jmol in the 
page when the user clicks a button these images would be put in the page with a 
button to click to "make interactive".  If the OS does not support JavaVMs the 
user would get a simple dialog message.

b) On the fly data sets are a little more difficult, but I have already 
implemented something for the SageMath package.  The latest version of 
JmolData.jar can be run headless on the server to generate image files.  I 
still need to work out generating the animated .gifs.  Ideally this would be 
something we could embed in JmolData.jar, but initially it could be output of 
image files and then use another package to make them into an animated .gif.

3) We could also investigate a javascript viewer version, that doesn't have 
capabilities to change a view, but could display it interactively.  Like 2b 
above this puts a lot of potential load on the server and bandwidth.

Some random ideas to start discussions

Jonathan
On Mar 29, 2012, at 7:41 AM, jmol-users-requ...@lists.sourceforge.net wrote:

> Message: 6
> Date: Thu, 29 Mar 2012 07:41:47 -0500
> From: Robert Hanson 
> Subject: Re: [Jmol-users] "Jmol" for iPads?
> To: jmol-users@lists.sourceforge.net
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
> 
> On Wed, Mar 28, 2012 at 9:19 PM, Craig T Martin wrote:
> 
>> Bob,
>> 
>>   I wouldn't be so dismissive of the iPad/iPhone revolution. Clearly the
>> latter looks to be dominating the smart phone market, despite it's higher
>> price tag. It wasn't that long ago that experts were dismissive of Apple
>> overall (or dismissive of mice and the GUI, for that matter). jmol risks
>> being left behind if it is not adapted to a platform with a growing user
>> base. I do appreciate that Apple's omitting Java support has made adapting
>> jmol very challenging, but I would love someone to rise to this challenge -
>> for my own and for jmol's sake.
>> 
>> 
> It's not that I'm dismissive. Apple appeals strongly to the early adopter
> community -- I understand that. But before you jump for a new iPad, read
> the reviews of the iPad 3 and do consider the Android tablet instead. My
> son and I absolutely love our Samsung, and I can't IMAGINE trading it for
> an iPad. It's just hands down a better environment. Apple's a game changer
> company, but how much  of that fanatical enthusiasm is warranted for that
> particular platform when so many other tablet-based options are available
> and so more flexible? What exactly is the appeal of a tablet that is so
> restrictive when other alternatives are available that let you do what you
> really want to do?
> 
> Bob

Dr. Jonathan H. Gutow
Chemistry Depa

Re: [Jmol-users] "Jmol" for iPads?

[Rzepa, Henry S]

On 29 Mar 2012, at 14:39, Robert Hanson wrote:

> Not quite. I think we're mostly in agreement.

You are right there Bob!
> 
> I'm saying that one solution, if you want  to implement Jmol on a tablet,
> is to to Android. I'm not interested in getting into a debate here of
> "Apple vs. Android." People have their passions.  I was just reacting to
> Craig's urge to go out and get an iPad, suggesting there are alternatives.
> 
> I think what I'm saying is that Jmol is now in a state that whoever wants
> to develop it for the iPad is clear to do so. The Android port shows that
> the Jmol library is totally independent of graphics environment, and people
> are coming up with solutions that port Java to iPad-based languages. All
> the pieces are there that are needed, as far as I can see.  What a
> developer would  need to do is replace one package (org.jmol.awt) with
> whatever works on their platform, and work that into a new GUI.  You don't
> have to give up the functionality of Jmol or feel like Jmol is a dead end
> because it is a Java program anymore. Whether or not someone wants to work
> on that, that's another question. Personally, I'm not planning on becoming
> an iPad developer.
> 
> But there are other fine solutions for the iPad. WebGL is great for simple
> displays of simple models. (I have yet to see ChemDoodle not crash on large
> proteins. I haven't seen surfaces yet from ChemDoodle, either. Maybe they
> just haven't had time; maybe it's not possible/practical. I don't know. I
> think they have other priorities, and if you can send me a link to surfaces
> from ChemDoodle, I'd be interested in coming up to speed with their
> environment. I note that ChemDoodle runs most effectively when connected to
> their site, which uses Java.)

Takanori Nakane  is working on  Surfaces, and he expressed much interest in 
.jvxl  It might be worth spinning that aspect out?


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Re: [Jmol-users] "Jmol" for iPads?

[Robert Hanson]

Not quite. I think we're mostly in agreement.

I'm saying that one solution, if you want  to implement Jmol on a tablet,
is to to Android. I'm not interested in getting into a debate here of
"Apple vs. Android." People have their passions.  I was just reacting to
Craig's urge to go out and get an iPad, suggesting there are alternatives.

I think what I'm saying is that Jmol is now in a state that whoever wants
to develop it for the iPad is clear to do so. The Android port shows that
the Jmol library is totally independent of graphics environment, and people
are coming up with solutions that port Java to iPad-based languages. All
the pieces are there that are needed, as far as I can see.  What a
developer would  need to do is replace one package (org.jmol.awt) with
whatever works on their platform, and work that into a new GUI.  You don't
have to give up the functionality of Jmol or feel like Jmol is a dead end
because it is a Java program anymore. Whether or not someone wants to work
on that, that's another question. Personally, I'm not planning on becoming
an iPad developer.

But there are other fine solutions for the iPad. WebGL is great for simple
displays of simple models. (I have yet to see ChemDoodle not crash on large
proteins. I haven't seen surfaces yet from ChemDoodle, either. Maybe they
just haven't had time; maybe it's not possible/practical. I don't know. I
think they have other priorities, and if you can send me a link to surfaces
from ChemDoodle, I'd be interested in coming up to speed with their
environment. I note that ChemDoodle runs most effectively when connected to
their site, which uses Java.)

One could easily tweak the page-based ChemDoodle library to point to any
other site, and have that site running Jmol in the background to do the
heavy lifting. Since the iPad is fundamentally based on being connected,
this is a very simple Jmol-based iPad solution that takes almost nothing
to implement -- just set up your own server and change one line in the
ChemDoodle code. I happen to think that's a fine solution for the iPad.

The main  problem with ChemDoodle developers is their philosophy that it
should not be scriptable. To my knowledge, is not scriptable, at least.
Sure, you can make JavaScript calls using matrices to do rotations and
such, but that's not what I mean. What Jmol has over every other web-based
molecular graphics option is scriptability. If you don't need that, there's
little need for Jmol. I think the sort of applications that people are
talking about -- books that show a 3D model that can be twiddled -- have
plenty of other options at their disposal than Jmol, and Jmol wouldn't
necessarily be the best option even if it were available, because for that
you don't need anything more than a few simple WebGL calls.

Bob


On Thu, Mar 29, 2012 at 8:08 AM, Rzepa, Henry S wrote:

>
> But Bob, you are saying that the solution to  Jmol on a tablet is to go
>  Android (and keep  Java).   I think others are saying there may be a
> second choice for the future as well, which may or may not involve an
> evolution of  Jmol.
>




>
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Re: [Jmol-users] "Jmol" for iPads?

[Rzepa, Henry S]

On 29 Mar 2012, at 13:41, Robert Hanson wrote:

> On Wed, Mar 28, 2012 at 9:19 PM, Craig T Martin wrote:
> 
>> Bob,
>> 
>>   I wouldn't be so dismissive of the iPad/iPhone revolution. Clearly the
>> latter looks to be dominating the smart phone market, despite it's higher
>> price tag. It wasn't that long ago that experts were dismissive of Apple
>> overall (or dismissive of mice and the GUI, for that matter). jmol risks
>> being left behind if it is not adapted to a platform with a growing user
>> base. I do appreciate that Apple's omitting Java support has made adapting
>> jmol very challenging, but I would love someone to rise to this challenge -
>> for my own and for jmol's sake.
>> 
>> 
> It's not that I'm dismissive. Apple appeals strongly to the early adopter
> community -- I understand that. But before you jump for a new iPad, read
> the reviews of the iPad 3 and do consider the Android tablet instead. My
> son and I absolutely love our Samsung, and I can't IMAGINE trading it for
> an iPad. It's just hands down a better environment. Apple's a game changer
> company, but how much  of that fanatical enthusiasm is warranted for that
> particular platform when so many other tablet-based options are available
> and so more flexible? What exactly is the appeal of a tablet that is so
> restrictive when other alternatives are available that let you do what you
> really want to do?

Thanks Bob.  You address a complex issue.   Amongst the other aspects are 

1. Do you want a QA controlled (by Apple) environment,  or  the more 
advertising-oriented environment of Android?
2. Which app store best contains the kind of apps that you want?
3. Allegedly,  Android apps  are often less battery friendly than  iPad apps 
(they need to advertise, not save your battery)
4. Security, again allegedly, is lower on Android.
5. iPad is not fragmented,  but  Android is device fragmented (unless of course 
you consider  Samsung as the only alternative player).
6. Few Android devices update the OS as often as  Apple does IOS. 
7. Is Apple's iCloud attractive to you?
8. Siri does recognise spoken chemical names (I have seen this demoed). Is this 
important to you?

But Bob, you are saying that the solution to  Jmol on a tablet is to go  
Android (and keep  Java).   I think others are saying there may be a second 
choice for the future as well, which may or may not involve an evolution of  
Jmol.
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Re: [Jmol-users] "Jmol" for iPads?

[Robert Hanson]

On Wed, Mar 28, 2012 at 9:19 PM, Craig T Martin wrote:

> Bob,
>
>I wouldn't be so dismissive of the iPad/iPhone revolution. Clearly the
> latter looks to be dominating the smart phone market, despite it's higher
> price tag. It wasn't that long ago that experts were dismissive of Apple
> overall (or dismissive of mice and the GUI, for that matter). jmol risks
> being left behind if it is not adapted to a platform with a growing user
> base. I do appreciate that Apple's omitting Java support has made adapting
> jmol very challenging, but I would love someone to rise to this challenge -
> for my own and for jmol's sake.
>
>
It's not that I'm dismissive. Apple appeals strongly to the early adopter
community -- I understand that. But before you jump for a new iPad, read
the reviews of the iPad 3 and do consider the Android tablet instead. My
son and I absolutely love our Samsung, and I can't IMAGINE trading it for
an iPad. It's just hands down a better environment. Apple's a game changer
company, but how much  of that fanatical enthusiasm is warranted for that
particular platform when so many other tablet-based options are available
and so more flexible? What exactly is the appeal of a tablet that is so
restrictive when other alternatives are available that let you do what you
really want to do?

Bob
-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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] "Jmol" for iPads?

[Adrià Cereto Massagué]

El 29 de març de 2012 4:19, Craig T Martin  ha
escrit:

>  I wouldn't be so dismissive of the iPad/iPhone revolution. Clearly the
> latter looks to be dominating the smart phone market, despite it's higher
> price tag.


That may be true in the USA, but not in Europe or the rest of America.
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Re: [Jmol-users] "Jmol" for iPads?

[Rzepa Henry]

On 29 Mar 2012, at 03:19, Craig T Martin wrote:

> Bob,
> 
>   I wouldn't be so dismissive of the iPad/iPhone revolution. Clearly the 
> latter looks to be dominating the smart phone market, despite it's higher 
> price tag. It wasn't that long ago that experts were dismissive of Apple 
> overall (or dismissive of mice and the GUI, for that matter). jmol risks 
> being left behind if it is not adapted to a platform with a growing user 
> base. I do appreciate that Apple's omitting Java support has made adapting 
> jmol very challenging, but I would love someone to rise to this challenge - 
> for my own and for jmol's sake.
> 
>   For those of you starting to use iPads in lecture, I do have some 
> colleagues at UMass who have an acceptable kludge, wherein they mirror their 
> laptops onto the iPad and then switch to that when they want to use jmol 
> structures (they can do everything else on the iPad and it is significantly 
> cheaper than the ThinkPads we used to use - not to mention a lot less buggy). 
> If anyone is interested, I can point them to my colleagues. But of course 
> this is not a general solution. 
> 
>   I don't yet have an iPad personally, but it's on my list of things to buy 
> next and I have a number of colleagues who are absolutely fanatical. Tomorrow 
> we go to the Dean to pitch an idea that will involve the purchase of 200 
> iPads, for laboratory and evening exam use. The latter would benefit greatly 
> from jmol adaptation.
> 
> Anyone game to take this on? Bringing jmol out of Java and into HTML5/OpenGL?

Someone else has already noted  GLMol,  
http://webglmol.sourceforge.jp/index-en.html  It is produced by Takanori Nakane 
(not sure if he reads this list) and I did not find it difficult to incorporate 
into an article (actually Peter Murray-Rust and I call these things datuments) 
I have just submitted to J Cheminformatics (ask me if you want a  "preprint"). 
OK, it does not actually yet display on an iPad (since for their own reasons 
Apple have not actually enabled it in IOS yet) but it is expected to as they 
say any day, as is  Android.

Takanori is currently working on implementing surfaces (and  I point out to him 
the wonderful  jvxl that  Bob has created); the list of other capabilities is 
also quite impressive. ChemDoodle web components too are impressive (as  I 
understand it, its core javascript functionality is open source) although a 
different model operates here (much of the advanced functionality is actually 
server side, and hence requires the user to have access to that server, and of 
course also be in online mode, ie it may eat up into any data plan you might 
have on eg your iPad).  My point is that these alternatives,  adopting as they 
do  HTML5 canvas and  WebGL,  are starting to appear. Whilst they are still 
years away from the functionality of  Jmol, they are going to increasingly  
make an impact.   

Let me give one example: if you are following  e-books you might appreciate the 
significance of the press release announcing that  ChemDoodle and  Inkling have 
partnered. I am convinced that "books" are now at the end of the induction 
period in evolutionary terms and they will now break out.  Jmol (to my 
knowledge) has not yet been incorporated into any  e-book (epub2, the current 
open format for these does not support scripting, but epub3, on which  Apple 
based their new ibooks, does), but  one can imagine that within a year there 
will be chemistry text books offering  Jmol-style interactivity. Given that the 
target device is Android/IOS, it seems  Jmol will not immediately feature in 
this revolution.   So  I agree with the statement above that Jmol risks being 
left behind.
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Re: [Jmol-users] "Jmol" for iPads?

[Egon Willighagen]

On Thu, Mar 29, 2012 at 4:19 AM, Craig T Martin  wrote:
> I don't yet have an iPad personally, but it's on my list of things to buy
> next and I have a number of colleagues who are absolutely fanatical.
> Tomorrow we go to the Dean to pitch an idea that will involve the purchase
> of 200 iPads, for laboratory and evening exam use. The latter would benefit
> greatly from jmol adaptation.
>
> Anyone game to take this on? Bringing jmol out of Java and into
> HTML5/OpenGL?

Why not pitch that idea you with Dean too then? Closed platforms do
come with a more limited amount of software... why not ask for
permission to purchase development time for someone to write this code
transition?

Egon

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PubList: http://www.citeulike.org/user/egonw/tag/papers

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Re: [Jmol-users] "Jmol" for iPads?

[Craig T Martin]

Bob,

   I wouldn't be so dismissive of the iPad/iPhone revolution. Clearly the 
latter looks to be dominating the smart phone market, despite it's higher price 
tag. It wasn't that long ago that experts were dismissive of Apple overall (or 
dismissive of mice and the GUI, for that matter). jmol risks being left behind 
if it is not adapted to a platform with a growing user base. I do appreciate 
that Apple's omitting Java support has made adapting jmol very challenging, but 
I would love someone to rise to this challenge - for my own and for jmol's sake.

   For those of you starting to use iPads in lecture, I do have some colleagues 
at UMass who have an acceptable kludge, wherein they mirror their laptops onto 
the iPad and then switch to that when they want to use jmol structures (they 
can do everything else on the iPad and it is significantly cheaper than the 
ThinkPads we used to use - not to mention a lot less buggy). If anyone is 
interested, I can point them to my colleagues. But of course this is not a 
general solution. 

   I don't yet have an iPad personally, but it's on my list of things to buy 
next and I have a number of colleagues who are absolutely fanatical. Tomorrow 
we go to the Dean to pitch an idea that will involve the purchase of 200 iPads, 
for laboratory and evening exam use. The latter would benefit greatly from jmol 
adaptation.

Anyone game to take this on? Bringing jmol out of Java and into HTML5/OpenGL?

Craig Martin
UMass Amherst Chemistry

PS - my kid's elementary school is 100% Apple. The middle and high school are 
mixed about 50/50.

PPS - conflict of interest statement here - I own Apple stock  ;-)

> Message: 1
> Date: Fri, 23 Mar 2012 16:42:10 -0500
> From: Robert Hanson 
> Subject: Re: [Jmol-users] "Jmol" for iPads?
> To: jmol-users@lists.sourceforge.net
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Jmol is now portable to the iPad. In principle, at least. The Android port
> shows that. But really, developing for the iPad is to develop something
> very different in behavior to what you have now, and I think there are
> different solutions, then, for that. You can't just take something like
> Jmol and expect it to 'run' on the iPad. What you want is something with
> the look and feel of an iPad. lots of gestures, no keyboard to speak of,
> just the essentials.
> 
> With all the other cheaper options out there, I'm sorry to see high
> schools are jumping for another round of Apple-ware. Funny how all the
> schools i've been in lately are filled with Windows machines even though a
> few years ago it was all Mac. I wonder why.
> 
> Bob
Craig Martin
cmar...@chem.umass.edu



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Re: [Jmol-users] "Jmol" for iPads?

[Robert Hanson]

Jmol is now portable to the iPad. In principle, at least. The Android port
shows that. But really, developing for the iPad is to develop something
very different in behavior to what you have now, and I think there are
different solutions, then, for that. You can't just take something like
Jmol and expect it to 'run' on the iPad. What you want is something with
the look and feel of an iPad. lots of gestures, no keyboard to speak of,
just the essentials.

With all the other cheaper options out there, I'm sorry to see high
schools are jumping for another round of Apple-ware. Funny how all the
schools i've been in lately are filled with Windows machines even though a
few years ago it was all Mac. I wonder why.

Bob

On Fri, Mar 23, 2012 at 4:32 PM, Thomas Stout wrote:

>
> There is also a version of Cuemol for the iphone and iPad
> http://itunes.apple.com/us/app/cuemol/id496236710?mt=8
>
> It is a viewer for content developed on a workstation with an "authoring"
> version of the program.
>
> It still has a ways to go, but seems to have potential
>
>
>
>
> On Fri, Mar 23, 2012 at 12:33 PM, Eric Martz wrote:
>
>> I just heard a segment on NPR about hundreds of high schools that are
>> abandoning textbooks and giving every student an iPad instead. As we
>> all know, iPads will not run java and so will not run Jmol. What are
>> people's thoughts on porting Jmol to a non-java language that would
>> run on a wider range of hardware/OS? And maybe have faster graphics
>> with open GL?
>>
>> -Eric
>>
>>
>>
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>
>
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Re: [Jmol-users] "Jmol" for iPads?

[Thomas Stout]

There is also a version of Cuemol for the iphone and iPad
http://itunes.apple.com/us/app/cuemol/id496236710?mt=8

It is a viewer for content developed on a workstation with an "authoring"
version of the program.

It still has a ways to go, but seems to have potential



On Fri, Mar 23, 2012 at 12:33 PM, Eric Martz wrote:

> I just heard a segment on NPR about hundreds of high schools that are
> abandoning textbooks and giving every student an iPad instead. As we
> all know, iPads will not run java and so will not run Jmol. What are
> people's thoughts on porting Jmol to a non-java language that would
> run on a wider range of hardware/OS? And maybe have faster graphics
> with open GL?
>
> -Eric
>
>
>
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Re: [Jmol-users] "Jmol" for iPads?

[lochana menikarachchi]

openSoft's IMolView for ipad - pretty fast and responsive


http://www.molsoft.com/iMolview.html
 



 From: Philip Bays 
To: jmol-users@lists.sourceforge.net 
Sent: Friday, March 23, 2012 4:41 PM
Subject: Re: [Jmol-users] "Jmol" for iPads?
 
At the ACS meeting last fall, someone was showing a version of Spartan on the 
iPad.  It was merely the builder and viewer.  The idea, as I remember it, was 
to be able to submit computations to a server and retrieve and display the 
results.  I do not know whether that is being pursued, and if so what the 
status is.  I realize that Spartan is not a Java program; it is simply to say 
that someone is thinking about a non-java implementation of some level of 
molecular modeling on the iPad.  Of course, for the age level of the classroom 
described in the article, advanced Spartan QM calculations would not be 
inappropriate.



On Mar 23, 2012, at 3:33 PM, Eric Martz wrote:

> I just heard a segment on NPR about hundreds of high schools that are 
> abandoning textbooks and giving every student an iPad instead. As we 
> all know, iPads will not run java and so will not run Jmol. What are 
> people's thoughts on porting Jmol to a non-java language that would 
> run on a wider range of hardware/OS? And maybe have faster graphics 
> with open GL?
> 
> -Eric
> 
> 
> --
> This SF email is sponsosred by:
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J. Philip Bays
Emeritus Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu






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Re: [Jmol-users] "Jmol" for iPads?

[Timothy Driscoll]

> On Mar 23, 2012, at 3:33 PM, Eric Martz wrote:
> 
>> I just heard a segment on NPR about hundreds of high schools that are 
>> abandoning textbooks and giving every student an iPad instead. As we 
>> all know, iPads will not run java and so will not run Jmol. What are 
>> people's thoughts on porting Jmol to a non-java language that would 
>> run on a wider range of hardware/OS? And maybe have faster graphics 
>> with open GL?
>> 

you might check out Molecules:



I've played with it on occasion, but haven't looked into details. I do know it 
uses openGL and is FOSS at the moment.



cheers,

tim
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Re: [Jmol-users] "Jmol" for iPads?

[Philip Bays]

At the ACS meeting last fall, someone was showing a version of Spartan on the 
iPad.  It was merely the builder and viewer.  The idea, as I remember it, was 
to be able to submit computations to a server and retrieve and display the 
results.  I do not know whether that is being pursued, and if so what the 
status is.  I realize that Spartan is not a Java program; it is simply to say 
that someone is thinking about a non-java implementation of some level of 
molecular modeling on the iPad.  Of course, for the age level of the classroom 
described in the article, advanced Spartan QM calculations would not be 
inappropriate.



On Mar 23, 2012, at 3:33 PM, Eric Martz wrote:

> I just heard a segment on NPR about hundreds of high schools that are 
> abandoning textbooks and giving every student an iPad instead. As we 
> all know, iPads will not run java and so will not run Jmol. What are 
> people's thoughts on porting Jmol to a non-java language that would 
> run on a wider range of hardware/OS? And maybe have faster graphics 
> with open GL?
> 
> -Eric
> 
> 
> --
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here 
> http://p.sf.net/sfu/sfd2d-msazure
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

J. Philip Bays
Emeritus Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu






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Re: [Jmol-users] "Jmol" for iPads?

[Angel Herráez]

Buzzwords... and politics. Who will be putting the cash for all those iPads? 
And how soon will 
they be obsolete?

I wonder how many (text)books are available for the iPad platform.

Regarding the reprogramming of Jmol, the task is not trivial (as Miguel and Bob 
will know), 
and who would do it? For profit, maybe?




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Re: [Jmol-users] "Jmol" for iPads?

[Egon Willighagen]

On Fri, Mar 23, 2012 at 8:33 PM, Eric Martz  wrote:
> I just heard a segment on NPR about hundreds of high schools that are
> abandoning textbooks and giving every student an iPad instead.

This is so sad... we're not even over the MS vendor lock-in, and ready
to buy into the next one...

Egon

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