Thanks very much. I do not know how I missed this in the FAQ. Gord
> Message: 7 > Date: Sat, 14 Jul 2007 06:43:07 -0500 (CDT) > From: [EMAIL PROTECTED] > Subject: Re: [Jmol-users] JmolViewer, Viewer > To: [email protected] > Cc: [email protected] > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain;charset=iso-8859-1 > > Try checking > > if(viewer.haveFrame()) > > first, just to see if there is a model loaded. ("Frame" in this context > refers to a model, recently refactored as "ModelSet", not a Java Frame.) I > think your problem may be that you have a viewer but no model set. That's > usually what a null pointer exception from a method such as > viewer.getAtomCount() means. In general, when you create a viewer, you > should also call > > setAppletContext(String htmlName, URL documentBase, URL codeBase, > String appletProxyOrCommandOptions) > > So a typical instantiation might be: > > JmolViewer viewer = JmolViewer.allocateViewer(display, modelAdapter); > viewer.setAppletContext("", null, null, ""); > > That second method includes a call to zap(), which instantiates a new > ModelSet, allowing viewer.getAtomCount() to return "0". > > Bob > > > >> I'm building a jmol embedded application which will allow me to open more >> than one molecules. Currently I'm able to open multiple molecules in a >> single application. However now I'm facing problems regarding Viewer. I >> have a jmolPanel which instantiate a SmarterJmolAdapter and also >> JmolViewer like what most people will do. I added this jmolPanel into a >> JInternalFrame (moleculeFrame) which will later be added to the main >> JDesktopPane. I have my own set of swing.GUi components that I want to >> use >> to access and manipulate the opened molecules which are shown in the >> jmolPanels contained in the moleculeFrames. Now the problem is whenever I >> try to access the viewer of each jmolPanel e.g viewer = >> (moleculeFrame.getJmolPanel()).getViewer();which will ask the jmolPanel >> of >> that particular moleculeFrame I'm referring to return the Viewer >> (JmolViewer).Then I tried to >> ...System.out.println(viewer.getAtomCount());I'm getting >> nullPointerException from the modelManager. I guess my Viewer is a >> null when I'm doing this, so any better way of instantiating the viewers >> in order to make it work?Help and advice will be very much >> appreciated.RegardsKevin >> _________________________________________________________________ >> Did you know you can now customize your mailbox with different colours to >> suit your mood with Windows Live Hotmail? >> http://get.live.com/mail/features------------------------------------------------------------------------- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/_______________________________________________ >> Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > > > ------------------------------ > > Message: 8 > Date: Sat, 14 Jul 2007 06:47:48 -0500 (CDT) > From: [EMAIL PROTECTED] > Subject: Re: [Jmol-users] mopac2007 images > To: [email protected] > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain;charset=iso-8859-1 > > note comments at > > http://openmopac.net/manual/trouble_shooting.html#visualize%20results > > > >> On 7/10/07, Gordon Ayers <[EMAIL PROTECTED]> wrote: >>> I have installed Jmol 11.2.4 on my windows XP machine and am having a >>> problem displaying Mopac2007 files. When I open a *.out >>> file it appears to load but nothing is in the display window of Jmol. >>> I also tried loading a *gpt file with the same result. What am I doing >>> wrong? >> >> It might very likely be that there is something particular about your >> Mopac2007 file format. The best thing you can do, is make a demo .out >> file, for example for water or methane or so, using the parameters you >> would use otherwise too, and send this output to the list, or upload >> it into the bug track system, and assign it LGPL license (copyright >> remains with you), so that we can redistribute it in our SVN, and use >> it for future testing purposes. >> >> Egon >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > > > ------------------------------ > > Message: 9 > Date: Wed, 18 Jul 2007 11:41:59 +0200 > From: Christian Baerlocher <[EMAIL PROTECTED]> > Subject: [Jmol-users] select/ignore with cavity in Jmol 11.2.4 > To: [email protected] > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hi, > > I have upgraded to Jmol 11.2.4 and now my script for the cavity > drawings in zeolites does not work properly anymore. > > I load two models from an xyz file and select the models using > something like this > > isosurface channel resolution 2.0 select (*/2) ignore (*/1) minset > 1000 POCKET cavity 1.0 sasurface 0.2 > > I works fine if you draw the channels for model one, but for model 2 > it seems to mix model 1 into it as well. > > It works also fine for both models for the "normal" isosurfaces. > > Has anything changed with select/ignore in the new version? I have > tried several options but none seems to work > > I use Jmol.js > > Thanks for your help > > Christian > > > > > > ------------------------------ > > Message: 10 > Date: Wed, 18 Jul 2007 09:48:46 -0500 > From: EW Fedosky <[EMAIL PROTECTED]> > Subject: [Jmol-users] Jmol in a Spry Region > To: [email protected] > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="us-ascii" > > Has anyone had any experience calling on jmol.js from within an Adobe > Spry region? This seems to be problematic, I assume due to > conflicting/nested JavaScripting. Using an embedded applet instead > seems to work widely except with IE 6. > > Ideas or experience anyone? > > -- > EW Fedosky > > > Edward W. Fedosky > > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > > ------------------------------ > > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > End of Jmol-users Digest, Vol 14, Issue 6 > ***************************************** > > > -- > No virus found in this incoming message. > Checked by AVG Free Edition. > Version: 7.5.476 / Virus Database: 269.10.8/906 - Release Date: 17/07/2007 > 6:30 PM > > ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
