Applications Embedding Jmol - Revision history

AngelHerraez: fixing wrong characters due to change in charset during migration of the wiki; text recovered from the old server

2019-03-26T19:20:47Z

fixing wrong characters due to change in charset during migration of the wiki; text recovered from the old server

AngelHerraez: moving MoCalc into alphabetic order

2015-02-26T23:18:55Z

moving MoCalc into alphabetic order

Yodah134 at 12:13, 24 February 2015

2015-02-24T12:13:16Z

Tzontonel: /* Applications using Jmol */ Added a new application

2013-09-07T06:30:05Z

‎Applications using Jmol: Added a new application

Anonymous: Added PMOL

2012-06-21T13:53:44Z

Added PMOL

Ssorgatem: /* How to embed Jmol into an application */

2012-04-12T18:48:55Z

‎How to embed Jmol into an application

Martin.guetlein: /* Applications using Jmol */

2012-03-29T16:24:34Z

‎Applications using Jmol

AngelHerraez: Reverted edits by Paydayloans816 (talk) to last revision by AngelHerraez

2011-01-20T20:07:53Z

Reverted edits by Paydayloans816 (talk) to last revision by AngelHerraez

Anonymous at 22:37, 18 January 2011

2011-01-18T22:37:48Z

AngelHerraez: reverting edition by Ipadwallpaper (vandalism)

2010-11-08T19:55:43Z

reverting edition by Ipadwallpaper (vandalism)

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 * [http://homepage.mac.com/swain/Sites/Macinchem/page6/page6.html iBabel] - A GUI for cheminfomatics toolkit Openbabel, iBabel uses embeded applets to display structures.
 * [http://j-ice.sourceforge.net/ J-ICE] - a Jmol web-'''I'''nterface for '''C'''rystallographic and '''E'''lectronic Properties. J-ICE can deal with CASTEP, CRYSTAL09 (as well as 06, 03 and 98), QUANTUM ESPRESSO, VASP, Wien2k, FHI-aim, CIF, PDB and many others formats. Watch some videos [http://www.youtube.com/view_play_list?p=E9BA884CFAB82840 here].
-* [http://janocchio.sourceforge.net/ Janocchio] is an applet and application; in addition to using Jmol display capabilities, it calculates both H-H and H-C 3-bond  NMR coupling constants and NOEs from a three-dimensional structure. Â© Eli Lilly and Co. Open source and hosted af SF.
+* [http://janocchio.sourceforge.net/ Janocchio] is an applet and application; in addition to using Jmol display capabilities, it calculates both H-H and H-C 3-bond  NMR coupling constants and NOEs from a three-dimensional structure. © Eli Lilly and Co. Open source and hosted af SF.
 * [http://sourceforge.net/projects/mocalc2012/ MoCalc2012] is a Graphical User Interface for MOPAC, GAMESS(US), Firefly and ORCA that uses Jmol for displaying geometries, orbitals, surfaces, animations and vibrations using the Jmol scripting language.
 * [http://mw.concord.org/modeler/index.html Molecular Workbench] - A Molecular Simulation Tool.

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 * [http://j-ice.sourceforge.net/ J-ICE] - a Jmol web-'''I'''nterface for '''C'''rystallographic and '''E'''lectronic Properties. J-ICE can deal with CASTEP, CRYSTAL09 (as well as 06, 03 and 98), QUANTUM ESPRESSO, VASP, Wien2k, FHI-aim, CIF, PDB and many others formats. Watch some videos [http://www.youtube.com/view_play_list?p=E9BA884CFAB82840 here].
 * [http://janocchio.sourceforge.net/ Janocchio] is an applet and application; in addition to using Jmol display capabilities, it calculates both H-H and H-C 3-bond  NMR coupling constants and NOEs from a three-dimensional structure. Â© Eli Lilly and Co. Open source and hosted af SF.
 * [http://mw.concord.org/modeler/index.html Molecular Workbench] - A Molecular Simulation Tool.
 * [http://www.openprocessing.org/sketch/6939 PMOL] - A Processing sketch using JMOL to load Molecules, and Processing to visualize them.
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 * [http://taverna.sourceforge.net/ Taverna].
 * [http://purl.org/utwente/e59199 TouchMol] - molecular visualization on a multi-touch table, allowing up to 4 users to interact with a molecular model using their fingers. Video clips: [http://www.youtube.com/watch?v=P741FEkwR50] [http://www.youtube.com/watch?v=C3Iuoj0GBHg] [http://www.youtube.com/watch?v=xZ9l-L672OI] [http://www.youtube.com/watch?v=BtNcYKVHJF4]
 === How to embed Jmol into an application ===

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 * [http://taverna.sourceforge.net/ Taverna].
 * [http://purl.org/utwente/e59199 TouchMol] - molecular visualization on a multi-touch table, allowing up to 4 users to interact with a molecular model using their fingers. Video clips: [http://www.youtube.com/watch?v=P741FEkwR50] [http://www.youtube.com/watch?v=C3Iuoj0GBHg] [http://www.youtube.com/watch?v=xZ9l-L672OI] [http://www.youtube.com/watch?v=BtNcYKVHJF4]
 === How to embed Jmol into an application ===

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 * [http://pfaat.sourceforge.net/ PFAAT] - Protein Family Alignment Annotation Tool.
 * [http://homepage.mac.com/eludens/proyectos/htmls/proteinglimpseen.html ProteinGlimpse] is a free widget for visualizing macromolecules retrieved from the Protein Data Bank or from local disk. It is a dashboard application for Mac OS X that uses the JmolApplet.
 * [http://www.sagemath.org Sage] is a computational platform with the goal of providing a viable free and open-source alternative to Matlab, Maple, Mathematica and Magma.  It uses Jmol for its 3D interactive plotting.
 * [http://www.efamily.org.uk/software/dasclients/spice/spice.shtml Spice] - Spice is a DAS client for distributed annotation of protein sequences and structures. A java webstart version can be run from online.

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 * [http://janocchio.sourceforge.net/ Janocchio] is an applet and application; in addition to using Jmol display capabilities, it calculates both H-H and H-C 3-bond  NMR coupling constants and NOEs from a three-dimensional structure. Â© Eli Lilly and Co. Open source and hosted af SF.
 * [http://mw.concord.org/modeler/index.html Molecular Workbench] - A Molecular Simulation Tool.
 * [http://pfaat.sourceforge.net/ PFAAT] - Protein Family Alignment Annotation Tool.
 * [http://homepage.mac.com/eludens/proyectos/htmls/proteinglimpseen.html ProteinGlimpse] is a free widget for visualizing macromolecules retrieved from the Protein Data Bank or from local disk. It is a dashboard application for Mac OS X that uses the JmolApplet.

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 === How to embed Jmol into an application ===
-* A very good start is the [http://jmol.svn.sourceforge.net/viewcvs.cgi/jmol/trunk/Jmol/examples/basic/Integration.java?view=markup Integration.java] out of [http://jmol.svn.sourceforge.net/viewcvs.cgi/jmol/trunk/Jmol/ Jmol SVN].
+* A very good start is the [http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/examples/basic/org/jmol/Integration.java?revision=17001&view=markup Integration.java] out of [http://jmol.svn.sourceforge.net/viewcvs.cgi/jmol/trunk/Jmol/ Jmol SVN].
 * To see how [http://www.efamily.org.uk/software/dasclients/spice/spice.shtml Spice] is integrating Jmol, please have a look [http://www.derkholm.net/svn/repos/spice/trunk/src/org/biojava/spice/jmol/ here].
 * A special page is devoted to using Jmol as 3D viewer for CDK based projects: [[Jmol Cdk Integration]].

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 * [http://www.mathematik.uni-bielefeld.de/~CaGe/ CaGe] ([http://caagt.ugent.be/CaGe/ mirror]) - the "Chemical & abstract Graph environment" is a collection of graph generators for GNU Linux and Mac OS X, that uses Jmol as one of its visualizers.
 * [http://graphics.cs.brown.edu/research/chempad/ ChemPad] renders in Jmol 3D models calculated on-the-fly from a formula sketched by hand in a tablet PC.
 * [http://homepage.mac.com/swain/Sites/Macinchem/page6/page6.html iBabel] - A GUI for cheminfomatics toolkit Openbabel, iBabel uses embeded applets to display structures.
 * [http://j-ice.sourceforge.net/ J-ICE] - a Jmol web-'''I'''nterface for '''C'''rystallographic and '''E'''lectronic Properties. J-ICE can deal with CASTEP, CRYSTAL09 (as well as 06, 03 and 98), QUANTUM ESPRESSO, VASP, Wien2k, FHI-aim, CIF, PDB and many others formats. Watch some videos [http://www.youtube.com/view_play_list?p=E9BA884CFAB82840 here].

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-== Payday Loans - How To Pay Payday Loan In Installments ==
+Jmol users, please add here your favorite Java applications that embed Jmol.
-We know it is really important that we have the helping hand in our daily needs yet we cannot lean our help to our neighbor or relatives due to the reason that they have their needs also so to have you the assurance that you will have the helping hand in times of trouble then [http://www.aaaloanstore.com/ '''Payday Loans'''] from the company or various creditors are such the kind of loans that we need in times of unexpected events like having emergency bills. Not to worry if you think that you cannot repay this because you can pay it by installment. Paydays loans do have the steps wherein you can follow so that you will have the chance to pay it by installment. There is online paday loan where you can see the information that best help for you to learn how to pay loans through installment.
+* [http://bioclipse.net/ BioClipse].
-[http://www.aaaloanstore.com/ '''Payday Loans'''], in the first place on it you must bear in mind that even in short term loans there are danger that you will e encountering if you don't enough information on it. There are payday loans from credit company who offer high interest rate and for this you must avoid this it is because that this will give you more hassle. You must be able to ask your lender so that you will know the terms of your Paycheck Loan.
+Most interaction with Jmol will happen by sending RasmolScript - like commands to Jmol. This is nicely documented by the [http://jmol.svn.sourceforge.net/viewcvs.cgi/jmol/trunk/Jmol/examples/basic/Integration.java?view=markup Integration.java] example. It is also possible to get data back out of Jmol. This can be done by accessing the JmolViewer class. This might be replaced by an Interface in the future.

← Older revision		Revision as of 19:55, 8 November 2010
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−	~~== Ipad Wallpaper - Customize By Yourself ==~~
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−	If you want to know how to customize your ipad wallpaper of coarse there are guidelines to follow for you to arrive a good wallpaper.One of this is to select a photo enlargement . This is the most important step making customizing, it will help edit and crop the image to size. The next thing you will do is to find and decide on what size and on what image of yourÂ iPad wallpapers that find you more interesting to be use ofÂ because it will serve as your background and select on the export tab in the light room. Just relax and be able to have patient in doing it.
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−	On yourÂ [http://www.ipadwallpaper.com/ ipad wallpaper] the native resolution of an iPad is 1024x768 though you can be able to resize it so as to view it in portrait or landscape. On the image select 'All Sizes' and download it. You should however ensure that the resolution is higher than 768 so as to stretch on the entire screen and press and hold the image for about 3 seconds, release and select on save image that will appear in pop up image. In photos application, select the uploaded image, click on the export button and select use it as wallpaper. As you can see it is just easy to customize your Wallpapers so do and try it now.
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	{{Jmol_Applications_Sections}}		{{Jmol_Applications_Sections}}
	=== Applications using Jmol ===		=== Applications using Jmol ===