Re: [Jmol-users] R: Re: JSmol Question
Definitely. Use Firefox though. Make sure the file name indicates it's nature. So eg 1crn.pdb vs 1crn.pdb.gz. On Jan 25, 2013, at 12:17 AM, "pino.stricc...@libero.it" wrote: > Is it still possible to create a Jsmol page locally, make the changes and > then upload it? > With one of last version i downloaded i receive message error "unrecognized > file format". > Pino > -- > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, > MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current > with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft > MVPs and experts. ON SALE this month only -- learn more at: > http://p.sf.net/sfu/learnnow-d2d > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol update
Mike, I downloaded it like 2 hours ago and it unzipped well (Windows, WinZip) -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol update
Bob, Not sure if I'm the only one having this problem, but I can't get jsmol.zip to decompress properly. On OS X 10.8.2, Archive Utility hangs while trying to unzip it. I both hope and don't hope it's just me! :-P Cheers, Mike --- Michael Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign On Mon, Jan 21, 2013 at 11:21 PM, Robert Hanson wrote: > http://chemapps.stolaf.edu/jmol/jsmol.zip > > -- echo IMAGE > -- background IMAGE > -- partially compressed .js files > > (I think you must load an image from the host machine, not cross-domain.) > > I have Google Closure-compiled all the necessary JS*.js files into one > 200KB file, JSmol.min.js, which is demonstrated at > > http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm > > The compressed set includes JSmoljQuery.js, JSmolCore.js, JSmol.js, > JSmolApplet.js, JSmolControls.js, JSmolApi.js, and j2s/j2sjmol.js > > j2s/java/package.js and j2s/core/core.*.js files are also loaded as needed. > > My attempt at closure-compiling core.z.js was not successful. > > http://chemapps.stolaf.edu/jmol/jsmol/test2.htm is still there, and it > uses the uncompressed files. > > 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 > > > > -- > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, > MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current > with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft > MVPs and experts. ON SALE this month only -- learn more at: > http://p.sf.net/sfu/learnnow-d2d > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] R: Re: JSmol Question
Is it still possible to create a Jsmol page locally, make the changes and then upload it? With one of last version i downloaded i receive message error "unrecognized file format". Pino -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] jmol & shutter glasses
Dear Jmolers, I've been asked a question from a teacher who has access to a DLP3D video projector and corresponding shutter glasses. Is there a way to display stereo in Jmol with theses devices ? I think such discussions have already come their way on that list but I can't find them... Thanks Paul -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Fwd: Jmol iPad app
Begin forwarded message: > From: Robert Hanson > Date: January 24, 2013 4:14:54 PM GMT+02:00 > To: undisclosed-recipients:; > Subject: Jmol iPad app > > Dear Jmol users, > > The Jmol iPad app. The obvious next step, right? So, I'd like to start a > discussion with Jmol users and Jmol page developers. > > IF we were to work on an iPad app, what would it take to make it the "killer > app" that would equal Jmol as the "killer applet."? What is it that makes > Jmol/JSmol unique as an applet/JavaScript library? > > Some ideas: > > -- scriptability - One of Jmol's key features is its high-level scripting > language that lets both web developers and (knowledgeable) web users interact > with it in ways that Jmol developers ourselves haven't conceptualized. > > -- adaptability - Web page developers can put the applet in a context of > their own choosing, with all sorts of interesting content around the applet > that makes this particular page for a page visitor a particularly interesting > and unique interactive experience. > > Of these two, the first is probably very easy to implement in a Jmol app. > What about the second? > > My thinking goes like this: There are three groups: > > -- Jmol code developers (meaning those of us writing the Java code) > -- Jmol page developers (those using Jmol for their own creative ends using > the code and interfaces developed by the Jmol code developers) > -- Jmol users (those who visit the pages created by the Jmol page developers) > > If you think about it, that second category is what makes Jmol unique. There > are programs out there like pyMol and Mercury, and others that are created by > code developers and used by users. But what other programs involve the > middle category? I think of Adobe Flash as something like that. Is that it? > Jmol is more like Flash than it is like pyMol? Jmol provides the technology > that page developers can use to design a unique experience for their page's > visitors. This is what makes Jmol quite different from, say, a JavaScript > library that allows one to pop up a 3D model on a page and pretty much leaves > it at that. That's what the combination of controls and high-level scripting > gets us. Right? > > It seems to me, that if a "Jmol app" were to be valuable, it would still > involve this triad of involvement. Wouldn't it be a waste of time to develop > "just another molecule viewer" even if it is Jmol? That would be more like > morphing the Jmol application into an iPad app, not the Jmol applet. > > But how would we maintain that middle tier? > > One idea: The "Jmol app" by itself does little. But what it does do is > interact with a cloud-based server (or perhaps any web site?) to pull context > down and surround the viewer window with that context. So what a "Jmol > context developer" (I can't think of the analogy in terms of iPad apps, > because I don't think there is this category yet) would do would be to > develop an actual web page with an actual computer using a standard browser > and then through some sort of registered process upload, perhaps, a link to > that page along with a thumbnail image and a set of searchable keywords or > abstract. While that page could be viewed on the browser, some version of it > could also be viewed within the Jmol app. When the Jmol app is opened, it > would be like getting an index to all the Jmol pages in existence -- those > adapted to this iPad idea. The user would select the [what? -- applet? (does > sound about right...)] of choice and off they go. That "applet" would pull > context from the web, surround the Jmol window with that context, and there > you have it. > > What do you think? Feedback? Suggestions? > > 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 > -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol Question
On Thu, Jan 24, 2013 at 2:27 PM, Otis Rothenberger wrote:
> You might be right, but I think it's more subtle than that. From what I
> read, iPad Safari actually sends a hover event. You see it when you touch a
> link and hold for a second rather than click (a quick tap). The hold
> selects the link and brings up a hover box, albeit not the link title
> hover. I haven't tried it, but I bet a :hover style would override Safari's
> hover box to bring up your own hover hint. It's not just links. Hovering
> (touch hold) page html containers selects them and brings up a copy box.
>
I'm pretty sure "touch and hold" fires "double-click". That's certainly a
configuration option in Windows 8.
>
> So in the case of bond selection, I really think it's a touch followed by
> a tap. The bond hover circles do not display, so I make the model go
> translucent for a second to reinforce proper bond selection.
>
> At first, I put this all in the fun challenge category, but I must admit
> that I'm pleasantly surprised to find how well JSmol behaves on
> Safari/iPad. IPad/Chrome on the other hand is useless.
>
> iPad aside, I can't believe how easy it was to bring most of our virtual
> model kit functionality from Jmol applet to JSmol.
>
>
Yes. It does seem that the small molecular problem is solved -- the iPad
has the power to do it, and the entire set of Jmol commands is now
implemented. There is the issue of the 3 Mb download, but that's about it.
I don't see that as a make-it-or-break it issue.
Now that I have my hands on an iPad for a few days, I'm going to be doing
some speed testing to see just what it is Safari on the iPad does so
poorly. I find it hard to believe this is a processor issue. I suspect it's
a JavaScript optimization issue.
Bob
> Otis
>
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Jan 24, 2013, at 12:50 AM, Robert Hanson wrote:
>
> isn't that called a "double-click"? :)
>
>
> On Wed, Jan 23, 2013 at 9:56 PM, Otis Rothenberger
> wrote:
>
>> Bob,
>>
>> OK, finally. I was screwing up with missing quotes on the bind. I had
>> them in what I pasted below, but they were missing in my code.
>>
>> You can conformation rotate about a bond on an iPad. The hover on the
>> bond is a bit tricky, but there's a learnable rhythm involved -
>> touch/up/touch/up. It works pretty well with a stylus. What fun.
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>> On Jan 23, 2013, at 4:15 PM, Robert Hanson wrote:
>>
>> you can certainly use
>>
>> UNBIND LEFT
>>
>> to unbind LEFT-CLICK.
>>
>>
>>
>>
>> On Wed, Jan 23, 2013 at 7:34 AM, Otis Rothenberger > > wrote:
>>
>>> Bob,
>>>
>>> I've discovered that iPad actually has a hover that allows me to select
>>> a bond in JSmol prior to a conformation rotation. So this hover/click
>>> movement sets me up for conformation. I'm currently using the following
>>> binding for this:
>>>
>>> bind "CTRL-LEFT" "select WITHIN(BRANCH,{atomno=rot1}, {atomno=rot2}); if
>>> (_X < 250){select WITHIN(BRANCH,{atomno=rot2}, {atomno=rot1});}
>>> rotateSelected {atomno=rot1} {atomno=rot2} @{_DELTAY*.5}
>>>
>>> The rot1 and rot2 are set up by the bond selection. The 250 is my half
>>> my JSmol window width.
>>>
>>> The above binding (CTRL-LEFT) is useless on an iPad. Is there any way to
>>> temporarily unbind "LEFT" alone so that it can be bound to the above
>>> script? If not, do any other touch executions of the above come to mind?
>>>
>>> I'm assuming above that "LEFT" alone would equate to touch-drag on the
>>> iPad.
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.com
>>> http://chemagic.com
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
>>> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
>>> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
>>> MVPs and experts. ON SALE this month only -- learn more at:
>>> http://p.sf.net/sfu/learnnow-d2d
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>> --
>> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
>> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
>> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
>> MVPs and experts. ON SALE this month only -- learn
Re: [Jmol-users] JSmol Question
You might be right, but I think it's more subtle than that. From what I read,
iPad Safari actually sends a hover event. You see it when you touch a link and
hold for a second rather than click (a quick tap). The hold selects the link
and brings up a hover box, albeit not the link title hover. I haven't tried it,
but I bet a :hover style would override Safari's hover box to bring up your own
hover hint. It's not just links. Hovering (touch hold) page html containers
selects them and brings up a copy box.
So in the case of bond selection, I really think it's a touch followed by a
tap. The bond hover circles do not display, so I make the model go translucent
for a second to reinforce proper bond selection.
At first, I put this all in the fun challenge category, but I must admit that
I'm pleasantly surprised to find how well JSmol behaves on Safari/iPad.
IPad/Chrome on the other hand is useless.
iPad aside, I can't believe how easy it was to bring most of our virtual model
kit functionality from Jmol applet to JSmol.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jan 24, 2013, at 12:50 AM, Robert Hanson wrote:
> isn't that called a "double-click"? :)
>
>
> On Wed, Jan 23, 2013 at 9:56 PM, Otis Rothenberger
> wrote:
> Bob,
>
> OK, finally. I was screwing up with missing quotes on the bind. I had them in
> what I pasted below, but they were missing in my code.
>
> You can conformation rotate about a bond on an iPad. The hover on the bond is
> a bit tricky, but there's a learnable rhythm involved - touch/up/touch/up. It
> works pretty well with a stylus. What fun.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.com
> http://chemagic.com
>
>
>
>
> On Jan 23, 2013, at 4:15 PM, Robert Hanson wrote:
>
>> you can certainly use
>>
>> UNBIND LEFT
>>
>> to unbind LEFT-CLICK.
>>
>>
>>
>>
>> On Wed, Jan 23, 2013 at 7:34 AM, Otis Rothenberger
>> wrote:
>> Bob,
>>
>> I've discovered that iPad actually has a hover that allows me to select a
>> bond in JSmol prior to a conformation rotation. So this hover/click movement
>> sets me up for conformation. I'm currently using the following binding for
>> this:
>>
>> bind "CTRL-LEFT" "select WITHIN(BRANCH,{atomno=rot1}, {atomno=rot2}); if (_X
>> < 250){select WITHIN(BRANCH,{atomno=rot2}, {atomno=rot1});} rotateSelected
>> {atomno=rot1} {atomno=rot2} @{_DELTAY*.5}
>>
>> The rot1 and rot2 are set up by the bond selection. The 250 is my half my
>> JSmol window width.
>>
>> The above binding (CTRL-LEFT) is useless on an iPad. Is there any way to
>> temporarily unbind "LEFT" alone so that it can be bound to the above script?
>> If not, do any other touch executions of the above come to mind?
>>
>> I'm assuming above that "LEFT" alone would equate to touch-drag on the iPad.
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.com
>> http://chemagic.com
>>
>>
>>
>>
>>
>>
>>
>> --
>> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
>> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
>> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
>> MVPs and experts. ON SALE this month only -- learn more at:
>> http://p.sf.net/sfu/learnnow-d2d
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>> --
>> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
>> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
>> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
>> MVPs and experts. ON SALE this month only -- learn more at:
>> http://p.sf.net/sfu/learnnow-d2d___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> --
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
> MVPs and experts. ON SALE this month only -- learn more at:
> http://p.sf.net/sfu/learnnow-d2d
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo
