Re: [Jmol-users] surfaces and JVXL files
> > On Aug 18, 2006, at 9:24 PM, Bob Hanson wrote: > >> Frieda, what sort of surfaces are you particularly interested in >> displaying? >> >> Bob > > Solvent-accessible surfaces of macromolecules are what I am > accustomed to using vis Chime, hence what I am seeking to create. > However I have to admit that I am not aware of what the distinction > is between "isosurface" and solvent-accessible surface... There are two subtle distinctions now being made in Jmol -- "Solvent-accessible" which means the probe center position when rolled around the molecule. This is: isosurface SAsurface 1.2 where 1.2 is the solvent probe radius. "solvent-excluded" or "molecular" which means the set of all points on the solvent sphere that touch the Van der Waals radius along with the portions of the solvent sphere that form "caveties" when the solvent sphere touches the molecule at more than one point. This is: isosurface solvent 1.2 Both are called isosurfaces because they represent the points in space that have the same measurement, in this case the same distance from the solvent probe (and as described above). "SAsurface" display is far faster than "solvent" and probably what you want. Sorry, earlier I forgot about the SAsurface option. Bob > > Frieda > > > >> >> Frieda Reichsman wrote: >> >>> Hi All, >>> >>> I am interested in fast rendering of surfaces for large molecules. It >>> seems that Bob Hanson has invented a file format for this purpose, >>> called JVXL. I have seem Angel Herraez's and Bob's test pages for >>> surfaces, but I am still puzzled as to how to get started in doing >>> this. >>> >>> To create a JVXL surface file in Jmol, do you first have to load a >>> CUBE file into Jmol? I have started to read a little about CUBE files >>> but am unfamiliar with them. How do you generate a CUBE file? >>> >>> Frieda >>> >>> /// >>> >>> >>> Frieda Reichsman, PhD >>> >>> Molecules in Motion >>> >>> Interactive Molecular Structures >>> >>> http://www.moleculesinmotion.com >>> >>> >>> /// >>> >>> >>> >>> - >>> --- >>> >>> - >>> >>> Using Tomcat but need to do more? Need to support web services, >>> security? >>> Get stuff done quickly with pre-integrated technology to make your >>> job easier >>> Download IBM WebSphere Application Server v.1.0.1 based on Apache >>> Geronimo >>> http://sel.as-us.falkag.net/sel? >>> cmd=lnk&kid=120709&bid=263057&dat=121642 >>> >>> - >>> --- >>> >>> ___ >>> Jmol-users mailing list >>> Jmol-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >> >> >> -- >> --- >> Using Tomcat but need to do more? Need to support web services, >> security? >> Get stuff done quickly with pre-integrated technology to make your >> job easier >> Download IBM WebSphere Application Server v.1.0.1 based on Apache >> Geronimo >> http://sel.as-us.falkag.net/sel? >> cmd=lnk&kid=120709&bid=263057&dat=121642 >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > /// > > Frieda Reichsman, PhD > Molecules in Motion > Interactive Molecular Structures > http://www.moleculesinmotion.com > > /// > > > - > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Pop-up documentation not working on Mac
Same cheat. (Really just loading an HTML file.) It's not that pop-ups don't work, it's that pop-ups that dump HTML code to the window instead of sending a page do not work. If no one comes up with a solution for the Mac bug (I have to say) that prevents on the fly writing HTML directly to a new window and having a LiveConnect applet, I will consider it a loss and cheat as well. :) Bob > One further example of (working) UI in Jmol applets in a pop-up > window in Safari: > > On Angel Herraez's page, > http://biomodel.uah.es/pruebas/jmol/pop-up_Jmol/v6_1/pop-up_Jmol.htm > > - select the radio button for generating a pop-up > - then click the link to view the structure > > the UI controls work in that pop-up window on Safari. > > Frieda > /// > > Frieda Reichsman, PhD > Molecules in Motion > Interactive Molecular Structures > http://www.moleculesinmotion.com > > /// > > > - > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] CML and jmol
Greetings: I tried to load the sample crystals listed at http://www.xml-cml.org/dtdschema/cmlCore/EXAMPLES/ including CRYSTAL1.XML, crystal1.html, and crystal2.html. jmol loaded the latter two fine, but did not display the crystals. I am wondering if I need to add addtional markup than what is in the sample files or if I need to configure jmol properly. Regards, Assadullah __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] [cml/ccml-discuss] CML and jmol
Hi, Ok, here are some first observations... On Sunday 20 August 2006 22:58, Mir Mohammed Assadullah wrote: > Here are the fragments: > > CRYSTAL1.XML: > > > > units="angstrom">4.500 > units="angstrom">4.500 > units="angstrom">4.500 > units="degrees">90 > units="degrees">90 > units="degrees">90 > > > > xyzFract="0.0 0.0 0.0" xy2="+23.2 -21.0"/> > xyzFract="0.5 0.0 0.0"/> > > Jmol might not be happy about the namespace prefix yet, but will need to verify that tomorrow. A question: does it show no atoms at all? If it would one Na and one Cl then that would be expected, because Jmol does not 'do' the symmetry yet. > --- > crystal1.html: > > > > >units="units:angstrom">4.500 >units="units:angstrom">4.500 >units="units:angstrom">4.500 >units="units:degree">90 >units="units:degree">90 >units="units:degree">90 > > > >xyzFract="0.0 0.0 0.0" xy2="+23.2 -21.0"/> > xyzFract="0.5 0.0 0.0"/> > > > > > > ___ > > crystal2.html: > > > > 9.4620 > 8.3920 > 5.2210 > 90. > 110.1800 > 90. > > > >yFract="0.2747" zFract="0.2500"/> >yFract="0.9067" zFract="0.2500"/> >yFract="0.0935" zFract="0.2560"/> >yFract="0.0823" zFract="0.1406"/> >yFract="0.2671" zFract="0.3005"/> >yFract="0.9867" zFract="0.0583"/> > > In this fragment the namespaced unit cell dictRef's might be a problem, but would like to check that... Do unit cell axes for all examples? More on this later this week... Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] surfaces and JVXL files
On Aug 20, 2006, at 5:26 AM, Hens Borkent wrote:Isosurface became the name of the command in Jmol to generate surfaces, probably because the first surfaces were molecular orbitals. Orbitals do not have a particular size; the values of the function get smaller and smaller with distance from the molecule, and surfaces are created by connecting points with the same value. Hence isosurface. Same for electron density, for which an isosurface can be drawn that coincides more or less with the van der Waals surface. Or much smaller, or larger, depends on what feature you would like to show.To solvent accessible surfaces this doesn't apply. There is only one, given the radius of the solvent.However, all these surfaces, spheres and so on are currently created with the command isosurface.OK, very clear now! thanks much.Frieda ///Frieda Reichsman, PhDMolecules in MotionInteractive Molecular Structureshttp://www.moleculesinmotion.com/// - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Pop-up documentation not working on Mac
One further example of (working) UI in Jmol applets in a pop-up window in Safari:On Angel Herraez's page,http://biomodel.uah.es/pruebas/jmol/pop-up_Jmol/v6_1/pop-up_Jmol.htm- select the radio button for generating a pop-up - then click the link to view the structurethe UI controls work in that pop-up window on Safari.Frieda///Frieda Reichsman, PhDMolecules in MotionInteractive Molecular Structureshttp://www.moleculesinmotion.com/// - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Bioclipse 1.0 released
Hi Oja,Thanks for your reply.Any idea when Eclipse 3.2.1 might appear? I do not see anything on the Eclipse wiki that is helpful in that regard.I would not be developing Bioclipse - I enquired because I was interested in trying out Bioclipse to see if it would be useful in exploring macromolecules as I develop web-based Jmol tutorials. Any thoughts on that?FriedaOn Aug 17, 2006, at 8:45 AM, Ola Spjuth wrote:Hi Frieda,Bioclipse is developed in Java but relies on native SWT-libraries and hence we need to distribute one version for each OS.We have had problems exporting correct packages for Mac OS X due to a bug in Eclipse 3.2 and Apple's compatibility libraries, but this should be fixed in the next Eclipse release (3.2.1). It is still possible to develop Bioclipse on a Mac (I am!) with some limitations in functionality.We hope to be able to offer a binary Mac OS X release very soon!See the wiki page http://wiki.bioclipse.net/index.php?title=Bioclipse_on_Mac_OS_X for more information.Cheers, .../OlaOn Aug 16, 2006, at 16:18 , Frieda Reichsman wrote:Hi Ola,The Bioclipse download pages seem to say that Bioclipse is OS-independent. Can you tell me which version will run on Mac OSX? It seems one is marked for Linux and the other for Win...Frieda///Frieda Reichsman, PhDMolecules in MotionInteractive Molecular Structureshttp://www.moleculesinmotion.com///On Aug 11, 2006, at 10:26 AM, Ola Spjuth wrote:The Bioclipse team is proud to announce the release of Bioclipse 1.0, containing a Jmol plugin and a script editor for Jmol scripts with syntax highlighting and code assistance. Bioclipse [1] is a free, open source, workbench for chemo- and bioinformatics with powerful editing and visualization capabilities for molecules, sequences, proteins, spectra etc. The major features of version 1.0 are: * Import and export in various file formats* Visual editing of molecular 2D-structures* 3D-visualization of molecules and proteins* Editing and visualization of sequences and features (DNA, RNA, proteins etc)* Graphing and editing of various types of spectra, e. g. NMR, MS* Retrieval of resources (sequences, proteins, etc) from public data repositories* Scripting of 3D-visualizations with syntax highlighting and content assistance* PDB-editor with syntax highlighting for working with PDB files* CMLRSS-viewer for downloading chemical content published on the web using RSS-feeds* Integrated, searchable help-system* Hierarchical view of molecular and macromolecular substructures and calculation of chemical properties* Connection with external programs, e. g. PyMol Bioclipse is a rich client, which means it is run on your local computer but also gives the possibility to communicate with servers for data retrieval and computational services. The powerful plugin architecture is based on Eclipse[2], and results in a responsive, integrated user interface designed for simple and intuitive operations that at the same time is easy to extend with custom functionality. There is much ongoing work with Bioclipse and new features are constantly added. Please visit the Bioclipse Wiki [3] in order to get the latest information regarding the development. Bioclipse is available for download from Sourceforge [4]. [1] Bioclipse homepage: http://www.bioclipse.net[2] Eclipse: http://www.eclipse.org[3] Bioclipse Wiki: http://wiki.bioclipse.net[4] Sourceforge project site: http://sourceforge.net/projects/bioclipse/ -Using Tomcat but need to do more? Need to support web services, security?Get stuff done quickly with pre-integrated technology to make your job easierDownload IBM WebSphere Application Server v.1.0.1 based on Apache Geronimohttp://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642___Jmol-users mailing listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users -Using Tomcat but need to do more? Need to support web services, security?Get stuff done quickly with pre-integrated technology to make your job easierDownload IBM WebSphere Application Server v.1.0.1 based on Apache Geronimohttp://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642___Jmol-users mailing listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users ///Frieda Reichsman, PhDMolecules in MotionInteractive Molecular Structureshttp://www.moleculesinmotion.com/// - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM We
Re: [Jmol-users] Pop-up documentation not working on Mac
On Aug 20, 2006, at 5:13 AM, David Leader wrote: I've never looked at the Jmol console - thought it was for script entry, but perhaps it gives error feedback too),Hi David,The Jmol console gives excellent and abundant feedback following the command, set debugscript onIn this mode, Jmol responds to every command in one way or another. Great for debugging long script files. *The 'java console' was a convenience for pre-OSX Mac users, So this 'java console' must have been a Mac OS thing... The Java console I am using is provided by Java itself, and is accessed by using a Java preferences panel, where you can tell Java to open up its own console by default when it encounters an applet. The Java preferences interface can be opened by going to Applications/Utilities/Java/J2SE 5.0/Java PreferencesWhich brings to mind this question - does anyone know if there a way to re-set Java's memory to avoid the "Java.lang out of memory error" that results from re-loading a page with an applet many times?because on other platforms error messages are generally directed to 'system.out' which is the generic command line - in Windows it would be the DOS command line, in unix it would be the unix command line. It was built in to Netscape and IE5 (I think) as a place for system.out errors and exceptions to go to, and if you had trouble with an applet you could have a look at it to see what had happened. In OSX there was no longer a need for this and it was dropped, much to the initial puzzlement of many of us who were used to it.As far as _javascript_ is concerned, there is no mechanism for sending messages to system.out (perhaps for security reasons?) and, as the _javascript_ interpreter is built into the browser, one is reliant on the browser-maker or third parties building debugging consoles. That's why you'll see different error messages for the same _javascript_ error on different browsers.Yes, and it seems to me that Firefox provides a terrific js console, which usually gives much more specific and helpful error messages than Safari's. But I much prefer Safari's implementation of Jmol, so I only go to FF when I have an inscrutable js error in Safari's js console.Thanks for all the explaining, always good to supplement my knowledge of how Mac OS works.Frieda ///Frieda Reichsman, PhDMolecules in MotionInteractive Molecular Structureshttp://www.moleculesinmotion.com/// - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] surfaces and JVXL files
Hi Frieda > > Solvent-accessible surfaces of macromolecules are what I am accustomed > to using vis Chime, hence what I am seeking to create. However I have > to admit that I am not aware of what the distinction is between > "isosurface" and solvent-accessible surface... > Isosurface became the name of the command in Jmol to generate surfaces, probably because the first surfaces were molecular orbitals. Orbitals do not have a particular size; the values of the function get smaller and smaller with distance from the molecule, and surfaces are created by connecting points with the same value. Hence isosurface. Same for electron density, for which an isosurface can be drawn that coincides more or less with the van der Waals surface. Or much smaller, or larger, depends on what feature you would like to show. To solvent accessible surfaces this doesn't apply. There is only one, given the radius of the solvent. However, all these surfaces, spheres and so on are currently created with the command isosurface. Hens (At this time Bob is really crossing the ocean, but I wouldn't be surprised if he is reading his e-mail and working on Jmol. Or is it still out of the question to take a pencil, let alone your laptop with you?) - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
