[Jmol-users] Jmol Android released

Check it out! https://market.android.com/search?q=jmol&so=1 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

Re: [Jmol-users] Jmol Android released

Downloaded! Any chance browser applets could be set up to point to the Android application if browser support for Java fails...? I'd be willing to modify code I have for existing applets, but I'm not familiar with the innards of Jmol (and especially the Android app). Cheers, Mike --- Mike Evans O

Re: [Jmol-users] partial charges from UFF

>@1.atomType = "C_3" >@2.atomType = "H_" >@3.atomType = "H_" > >etc. > >then > >{atomtype="C_3"}.partialCharge = This is a manual variable assignment is it not? Would it be possible to assign the UFF atom types to the Jmol atomType (atom properties array) when a minimization is ru

Re: [Jmol-users] Reverse a compare animation? & DOCUMENTATION

Dear Bob, 1. Yes indeed, I am able to save and restore coordinates (and I did not know I could do that!). However, what I wanted is to animate the restore, not to have it snap to the final position all at once. Is there some way to do that? OK, here is a (crude?) idea. I am aligning a Salmonel

[Jmol-users] Mobile molecular viz via WebGL

I saw the notice about Jmol running on Android, which is great news. Wanted to mention that for us mobile device folks, WebGL is also moving forward, and could be a solution for browser-based mol viz on iOS. I wonder whether server-side WebGL and Jmol could be mated in some way - or perhaps a pu

Re: [Jmol-users] Jmol Android released

At 12/5/11, Bob wrote: >Check it out! > >https://market.android.com/search?q=jmol&so=1 > >Bob Bob, this is just INCREDIBLE! WOW! You continue to knock my socks off! (For those who haven't visited this site, Bob has put there a very cool short video

Re: [Jmol-users] Jmol Android released

On Mon, Dec 5, 2011 at 9:28 AM, Michael Evans wrote: > Downloaded! Any chance browser applets could be set up to point to the > Android application if browser support for Java fails...? YES! And the user would be directed to the Market if they do not have the app. > I'd be willing to modify c

Re: [Jmol-users] Jmol Android released

On Mon, Dec 5, 2011 at 1:08 PM, Eric Martz wrote: > At 12/5/11, Bob wrote: > >Check it out! > > > > > https://market.android.com/search?q=jmol&so=1 > > > >Bob > > > I guess getting Jmol on an Apple iPad is hopeless, tho? (We got an > iPad2 for my wife

Re: [Jmol-users] Mobile molecular viz via WebGL

That's pretty much called ChemDoodle. It's not the WebGL, it's the JavaScript that has to run it that is pretty low power. I have yet to see a large protein rendered well, and so far I have not seen 100,000 triangles for a surface rendered at all. My plan is to leave that to others. Frankly, I'll

Re: [Jmol-users] Jmol Android released

Right on...this page seems to suggest that you need to associate URLs or data types with your application in its AndroidManifest.xml file: http://stackoverflow.com/questions/2958701/launch-custom-android-application-from-android-browser Cheers, Mike --- Mike Evans Organic Chemistry Graduate Stud

Re: [Jmol-users] sending a screen shot back to a server.

Bob, this is intriguing : I'm not sure I understand it well... Do you mean that it's possible to install Jmol 12.3.8 on a server and use it to generate images ? Or is it possible to generate an image file form the applet, that would be sent to a server (which could send it back to the user) ? Pau

Re: [Jmol-users] Reverse a compare animation? & DOCUMENTATION

On Mon, Dec 5, 2011 at 12:56 PM, Eric Martz wrote: > Dear Bob, > > 1. Yes indeed, I am able to save and restore coordinates (and I did > not know I could do that!). However, what I wanted is to animate the > restore, not to have it snap to the final position all at once. Is > there some way to do

Re: [Jmol-users] sending a screen shot back to a server.

Paul, I mean that any applet can send back its view as PNG or PNGJ to the server. Very simple creation of images, at the size of the applet, at least. Just have the applet send it back! It is encoded base64, so you need to decode that at the other end. I had problems with PHP because it also decod

Re: [Jmol-users] Mobile molecular viz via WebGL

Hi Bob; I agree 100% with you about the rate limiting factor being the JavaScript, but as you can see, even on an iPad or the last version of iPhone, it's very fast for a small/medium sized structure. I think this is what surprised us here so much (not totally sure why, with good LOD implemented

Re: [Jmol-users] sending a screen shot back to a server.

(in my case an APPLICATION (MPJmolApp.jar) is sending its image to the server, not an applet, but it's the same idea. On Mon, Dec 5, 2011 at 3:13 PM, Paul Pillot wrote: > Bob, this is intriguing : I'm not sure I understand it well... > Do you mean that it's possible to install Jmol 12.3.8 on a s

Re: [Jmol-users] Mobile molecular viz via WebGL

On Mon, Dec 5, 2011 at 3:21 PM, Quinn, Greg wrote: > Hi Bob; > I agree 100% with you about the rate limiting factor being the JavaScript, > but as you can see, even on an iPad or the last version of iPhone, it's > very fast for a small/medium sized structure. I think this is what > surprised us

Re: [Jmol-users] partial charges from UFF

sounds like a great idea to me. atomType is not used for much, and this is really what it is for. No need to do the minimization -- we should be able to have minimize set atomType or something like that. On Mon, Dec 5, 2011 at 11:38 AM, Spinney, Richard < rspin...@chemistry.ohio-state.edu> wro

Re: [Jmol-users] sending a screen shot back to a server.

Thanks Bob, this is a great feature ! It means that we don't need anymore the jmolGetProperty imageData method to do that. (moreover, this is precisely the feature I needed for one of the project I'm working on) Is there any callback to this function (to know when the transmission has finished w

Re: [Jmol-users] sending a screen shot back to a server.

It is synchronous. Var x = load("http://..?POST?_PNG_";) can have any return your server wants to give it. I have my returning the number of bytes saved in the file (after decoding). Jmol will wait for the return. I know that looks like you are loading a page into "x", but you are really

Re: [Jmol-users] Mobile molecular viz via WebGL

ChemDoodle is proprietary, but Chemdoodle web components (that's what Bob referred to) is open source (GPL) It uses javascript and doesn't need Jmol on the server side. You can feed the script with a PDB file and it will eventually render it in the WebGL canvas (graphics are nice and fast on my

Re: [Jmol-users] Mobile molecular viz via WebGL

OK, that makes sense. Most importantly, at least the last time I talked with them, which was last summer, while they are eager to develop this further, developing a scripting language is not in their schema. So you get a model, but there's not a lot you can do with it. For example, you can't say "s