Re: [Jmol-users] Sharing of Jmol scripts? and Jmol's state script output
Hi Andreas (and others not aware of the awesome power of Jmol's state script), One thing is that when I typed 'state script' I meant the actual state that Jmol outputs and not a script that is just a list of commands. It is the 'state' you can copy from Jmol when you press the 'state' button in the console or "show---> current state" from the Jmol menu. It is the current state of everything on the screen at the moment and can be easily recorded (saved locally as text)/shared and can be pasted into Jmol to get back that view. I was referring to in my reply using the state script to take other Jmol views or scenes and copy them to Proteopedia. Proteopedia is an online site at www.proteopedia.org. It is a wiki project for structural biology. You can make Jmol scenes and share them with others or keep them private. The are stored on a server in Israel. To do what I am talking about see http://proteopedia.org/wiki/index.php/Help:Copying_FirstGlance_Scenes_into_Proteopedia The page that link takes you to is written for copying from FirstGlance in Jmol to Proteopedia but it actually is more general than that. It allows you to copy any Jmol state script from any instance of Jmol to any other instance of Jmol (even a local one in the application too), assuming you load the correct model into the Jmol to which you are copying. And since you don't want to trigger a 'load' command but do want to describe the scene fully otherwise, you comment the load command out. I have found that two slashes like '//' also work to comment out the load command. One problem can be if the versions happen to be vastly different but for most things it works. Another issue is that page (http://proteopedia.org/wiki/index.php/Help:Copying_FirstGlance_Scenes_into_Proteopedia) seems like it needs some updating because I think they fixed things in new versions so the 'state' button in the console indeed gives you the state. Hope this helps, Wayne -- Message: 3 Date: Mon, 9 Aug 2010 09:00:05 -0700 From: Andreas Prlic Subject: Re: [Jmol-users] Sharing of Jmol scripts? To: jmol-users@lists.sourceforge.net Message-ID: Content-Type: text/plain; charset=ISO-8859-1 Hi Wayne, Can you explain a bit more how the conversion STATE->jmol script conversion works? is this tool open source? Andreas On Sun, Aug 8, 2010 at 1:24 PM, Wayne Decatur wrote: > Hi Andreas, > I would posit that Proteopedia makes it possible to what you suggest > presently. If you use the scene authoring tools on each Proteopedia page to > create your Jmol scene and save it (to Proteopedia's server) you have done > what you seem to suggest. > If your state is coming from another instance of Jmol or a state you saved > locally > You load the appropriate pdb file in Proteopedia's Scene authoring tools and > paste into the console the state script from elsewhere (with load command > commented out) and save the resulting scene to your page with the data > residing on Proteopedia's server. > > Wayne > >>Date: Sun, 8 Aug 2010 11:49:09 -0700 >>From: Andreas Prlic >>Subject: Re: [Jmol-users] Sharing of Jmol scripts? >>To: jmol-users@lists.sourceforge.net > >>Related to this I was wondering if it is possible to upload the state >>of Jmol to a server. This could be similar to saving the state >>locally, but rather than writing the file, Jmol could post the state >>to a URL provided by the web site... >> >>Andreas > > -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Sharing of Jmol scripts?
Hi Wayne, Can you explain a bit more how the conversion STATE->jmol script conversion works? is this tool open source? Andreas On Sun, Aug 8, 2010 at 1:24 PM, Wayne Decatur wrote: > Hi Andreas, > I would posit that Proteopedia makes it possible to what you suggest > presently. If you use the scene authoring tools on each Proteopedia page to > create your Jmol scene and save it (to Proteopedia's server) you have done > what you seem to suggest. > If your state is coming from another instance of Jmol or a state you saved > locally > You load the appropriate pdb file in Proteopedia's Scene authoring tools and > paste into the console the state script from elsewhere (with load command > commented out) and save the resulting scene to your page with the data > residing on Proteopedia's server. > > Wayne > >>Date: Sun, 8 Aug 2010 11:49:09 -0700 >>From: Andreas Prlic >>Subject: Re: [Jmol-users] Sharing of Jmol scripts? >>To: jmol-users@lists.sourceforge.net > >>Related to this I was wondering if it is possible to upload the state >>of Jmol to a server. This could be similar to saving the state >>locally, but rather than writing the file, Jmol could post the state >>to a URL provided by the web site... >> >>Andreas > > > > > -- > This SF.net email is sponsored by > > Make an app they can't live without > Enter the BlackBerry Developer Challenge > http://p.sf.net/sfu/RIM-dev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Sharing of Jmol scripts?
Hi Andreas, I would posit that Proteopedia makes it possible to what you suggest presently. If you use the scene authoring tools on each Proteopedia page to create your Jmol scene and save it (to Proteopedia's server) you have done what you seem to suggest. If your state is coming from another instance of Jmol or a state you saved locally You load the appropriate pdb file in Proteopedia's Scene authoring tools and paste into the console the state script from elsewhere (with load command commented out) and save the resulting scene to your page with the data residing on Proteopedia's server. Wayne >Date: Sun, 8 Aug 2010 11:49:09 -0700 >From: Andreas Prlic >Subject: Re: [Jmol-users] Sharing of Jmol scripts? >To: jmol-users@lists.sourceforge.net >Related to this I was wondering if it is possible to upload the state >of Jmol to a server. This could be similar to saving the state >locally, but rather than writing the file, Jmol could post the state >to a URL provided by the web site... > >Andreas -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Sharing of Jmol scripts?
Related to this I was wondering if it is possible to upload the state of Jmol to a server. This could be similar to saving the state locally, but rather than writing the file, Jmol could post the state to a URL provided by the web site... Andreas On Sun, Aug 8, 2010 at 2:23 AM, Egon Willighagen wrote: > Hi all, > > I saw some interesting emails lately on the scripts and sorts... has > anyone yet considered using MyExperiment.org for sharing useful Jmol > scripts? > > Would that be an interesting platform to share Jmol scripts like: > > Show the heme groups in protein X. > Demonstrate the hydrogen bonding framework in alpha helices. > > Egon > > -- > Post-doc @ Uppsala University > Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg > Homepage: http://egonw.github.com/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > > -- > This SF.net email is sponsored by > > Make an app they can't live without > Enter the BlackBerry Developer Challenge > http://p.sf.net/sfu/RIM-dev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Sharing of Jmol scripts?
Hi all, I saw some interesting emails lately on the scripts and sorts... has anyone yet considered using MyExperiment.org for sharing useful Jmol scripts? Would that be an interesting platform to share Jmol scripts like: Show the heme groups in protein X. Demonstrate the hydrogen bonding framework in alpha helices. Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
