[Jmol-users] JmolViewer
Hi All, I was looking for a JmolViewer jar file that I can embed in a stand alone application. I can see JMol application and applet viewer in the downloads but not a jar file that can be used for developing a stand alone application. How do I go about this?? Thanks. Lochana -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Can I calculate hbonds using pop-up menu?
Thank you Ángel for your research. This works. I can show my students that hbonds feature works in the pop-up menu with pdb files and if they use mol2 files, it can be done via console. I think we continue with mol2 format because of the partial charge data and electrostatic potential surfaces included in mol2. We also need the multi frame feature at the course. Best regards Johannes 28.1.2012 13:51, Herráez Sánchez Ángel kirjoitti: Well, I have done a little research and yes, I can confirm Johannes' observation. Jmol 12.2.2 has also disabled the popup menu "calculate Hbonds" for MOL2 files, but not for PDB files. However, the ability to calculate is there in the script console. These "feature" is by design, since that popup menu subentry is in the source code part of a group being active only on PDB files. I am not sure is this can/should be overruled or what is the sensible solution in coding terms. Other options like "select> protein" etc. shpuld also be disabled, right? That is because formats other than PDB are not prepared to provide the necessary information. Could you get away from mol2 format? Maybe convert to pdb? Another possible way may be to build a custom menu http://wiki.jmol.org/index.php/Custom_Menus where you will add an option linked to the "hbonds calculate" script. -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Can I calculate hbonds using pop-up menu?
Well, I have done a little research and yes, I can confirm Johannes' observation. Jmol 12.2.2 has also disabled the popup menu "calculate Hbonds" for MOL2 files, but not for PDB files. However, the ability to calculate is there in the script console. These "feature" is by design, since that popup menu subentry is in the source code part of a group being active only on PDB files. I am not sure is this can/should be overruled or what is the sensible solution in coding terms. Other options like "select > protein" etc. shpuld also be disabled, right? That is because formats other than PDB are not prepared to provide the necessary information. Could you get away from mol2 format? Maybe convert to pdb? Another possible way may be to build a custom menu http://wiki.jmol.org/index.php/Custom_Menus where you will add an option linked to the "hbonds calculate" script. <>-- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Can I calculate hbonds using pop-up menu?
Hello Johannes As you may know, H-bond calculation in Jmol is limited to certain situations (mostly proteins) and has evolved (expanded) during the last years. I am not sure about your problem, first I thought it may be related to the file format not being pdb. But since you say that you can do it from the console, then it may be some kind of bug. Maybe there was a former limitation that has been removed in the script processor but not from the menu generator. Bob Hanson will be able to tell you. Anyway, have you tried with a pdb file, to see if there is a difference? I remember using the popup menu for calculate, so the ability is there. <>-- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
