Where we cross in the night, Kevin, is in what we imagine people wanting to
do with "scripting" I think. While people could tap into the core of JSmol
and learn how to manipulate the model directly, writing something that,
say, allowed the selection of atoms and then centered the display on them,
it's a lot easier to write:
Jmol.script(jmolApplet0, "select 10-20;center selected;display selected")
Right? My apologies to developers who would prefer to access the model
directly and not utilize these higher level scripting features.
I'm truly very interested in seeing actual pages that have been developed
using ChemDoodle 3D tools. All I can find are your two pages, Kevin:
http://web.chemdoodle.com/demos/pdb-ribbons
http://web.chemdoodle.com/demos/molgrabber-3d
Please point us to pages that others have developed that utilize some sort
of nontrivial manipulation of the model to good effect. I for one would be
very interested in what people have done with this tool. My problem is that
when I search for "ChemDoodle" I find only 2D drawing sites. What keywords
should I be using for that?
Another question: I'm struggling to understand how you envision the
HTML5-only and the WebGL versions of ChemDoodle 3D being used. How do you
see that working? Do you see the WebGL version as being at all usable at
this point -- based on the limited availability of WebGL? Is it still just
a proof-of-concept for a future when WebGL is ubiquitous? (Can the same be
said for HTML5?) What are the advantages to using one over the other?
Bob
On Mon, Jan 14, 2013 at 7:45 AM, Kevin Theisen <ke...@ichemlabs.com> wrote:
> Hi Bob,
>
> I get it, you are biased towards JSmol as I am biased towards the
> ChemDoodle Web Components. Certainly you are an authority on Jmol, but when
> it comes to the ChemDoodle Web Components and to WebGL your knowledge is
> lacking at best.
>
> I'm not interested in starting a flame war here, I only responded to
> correct the biased statement about our product.
>
> Jmol provides a tried and tested scripting language that many here are
> used to using. This is a good thing. But it is not the only way. The
> ChemDoodle Web Components use Javascript. You are always stating that you
> need to be a programming wizard to use even basic Javascript tools. I would
> be surprised if your users didn't find that a bit insulting. Everyone here
> is very smart and probably already knows how to use Javascript. With our
> tutorial the majority of the ChemDoodle Web Components API can be mastered
> within a few hours, allowing users significant control over the software
> and a very sophisticated and flexible ability to mold their HTML5
> interfaces.
>
> I am glad our developments in the HTML5 space over the last 4 years have
> inspired you to create JSmol. The open source community benefits from
> having access to many options. As I said before, regardless of our
> opinions, the community wins here, which is the real goal behind open
> source solutions. I am happy to contribute!
>
> Sincerely,
> Kevin Theisen
> President, iChemLabs
>
>
>
>
>
>
> On Jan 13, 2013, at 8:12 PM, Robert Hanson wrote:
>
>
>
>
> On Sun, Jan 13, 2013 at 4:59 PM, Kevin Theisen <ke...@ichemlabs.com>wrote:
>
>> Thanks for the analysis Bob, I need to add in my thoughts.
>>
>> First, as far as open source goes, I don't really believe there is any
>> sense of some "competition". Open source provides tools to the community,
>> each is unique and will be used in unique ways by the community. Some will
>> even use multiple solutions to craft the type of product they are trying to
>> create. Open source solutions are all great. In the open source world, if a
>> tool is not necessary, people will not use it and it will not be developed
>> further. But an open source developer that believes he/she is in some sort
>> of competition with another open source solution has already lost.
>>
>>
> I hope I didn't make that sound competitive. I was remarking about the
> tools that are out there that I know of. I'm very happy to see ChemDoodle
> continue to develop, and if what we have done helps in that, that's
> terrific. I'm just saying that right now it has such a long way to go to
> get to Jmol's level of sophistication, operability, and flexibility,
> whereas JSmol is there right now.
>
>
> And this is the only pointed question I have for you Bob, how do you see
>> the J(S)mol code being sustainable as time goes on? There will be users
>> that want offline desktop support, <canvas> support and WebGL support. Each
>> time you develop a feature, you have to re-implement it twice more or very
>> soon users will get confused as to which version to use. What is your
>> advice on this?
>>
>
> Well, actually, that's the beauty of it, Kevin. JSmol is Jmol. The
> codebase is the same, so new features are new features, that's all. It is
> highly sustainable. Not sure what you mean by "reimplementing". I push one
> button, and it becomes the Jmol Java application and the Jmol applet; I
> push another, and it becomes JavaScript. It's not as if I am developing
> these independently. I have not been developing JSmol as a new product; I
> have been adapting Jmol to be able to be compiled directly into either Java
> or JavaScript, that's all.
>
> The WebGL support is minimal simply because I have been reluctant to
> produce something that is only an approximation of the "real thing" so far.
> In contrast, the HTML5 version is an exact pixel-for-pixel reproduction of
> Jmol in JavaScript. It's the same code. I think the WebGL aspects will
> develop, if there is really interest in that, but I don't see it as a high
> priority right now. There is still just too little of a base for WebGL. For
> example, I just got a new Windows 8 computer, and both Chrome and MSIE
> refuse to view http://web.chemdoodle.com/demos/molgrabber-3d . Since
> iPads also don't have WebGL enabled, that's just not a workable solution.
> Maybe Apple will enable full HTML5 functionality, but I'm not interested in
> waiting for that.
>
> I'm not sure about your comment in relation to Jmol needing a server. What
> is that all about?Are you saying ChemDoodle is pulling files successfully
> off a hard drive without a server in MSIE and Chrome? Desktop Jmol is in
> the form of the Jmol application. Java is not disappearing from computers
> -- the issue isn't Java per se, it's Java as a plug-in to a browser.
>
> Kevin, a few questions for you:
>
> What is the platform base for ChemDoodle 3D now? I still can't find much
> that will run it.
>
> Is http://web.chemdoodle.com/demos/molgrabber-3d still a working page? (I
> can't get that to work, personally.)
>
> Do you have plans to support MSIE?
>
> Can you please point us to the page you had that lists web sites using
> ChemDoodle? I'm very interested in seeing what people are doing iw
>
> Bob
>
>
>>
>> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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