Re: [Jmol-users] Jmol-users Digest, Vol 38, Issue 11
Hi Robert, > I'm not sure I understand why two frames are necessary. You only have one > file, and you are only loading it once. I think your "frame 1.1" and "frame > 1.2" do nothing. Here's what I see: > > $ load c:/temp/nbo.gz filter "NBO" > The Resolver thinks Gaussian > filtering with ;NBO; > filter MOs: false for " molecular orbital coefficients " > Mulliken charges found for Model 1 > Molecular dipole for model 1 = (2.0E-4, 3.3087997, 1.0976) > Using NBO charges for Model 1 > 748 natural bond orbitals read > 748 molecular orbitals read in model 1 > > $ isosurface mo1 mo 15 > mo1 created with cutoff = 0.05 ; number of isosurfaces = 1 > color range -1.0 1.0; mapped data range -1.0 to 1.0 > $ isosurface mo2 mo 665 > mo2 created with cutoff = 0.05 ; number of isosurfaces = 2 > color range -1.0 1.0; mapped data range -1.0 to 1.0 > $ show frames all > > file["1.1"] = "c:/temp/nbo.gz" > title["1.1"] = "" > name["1.1"] = "E(RB+HF-LYP) = -3122.57031345 A.U." > > so there's only one frame. I was playing around with the overlap of the two orbitals for some time. Initially, I only had one frame, but somehow that stopped working (so it appeared) so tried two frames. I think the main problem I had was the cache of the browser which did not get updated the way I wanted it. I agree, one frame is enough. > > However, in order to switch from the single orbitals to the > > donor/acceptor view forth and back, I am currently reloading the > > molecule. > > You can just say > > isosurface delete > > to get rid of the current isosurfaces and start again. Certainly no need to > reload the file. Great! Thanks for the prompt reply! That is now working the way I wanted it!. All the best from Glasgow! Jörg -- * Jörg Saßmannshausen Research Fellow University of Strathclyde Department of Pure and Applied Chemistry 295 Cathedral St. Glasgow G1 1XL email: jorg.sassmannshau...@strath.ac.uk web: http://sassy.formativ.net Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Command Line Bug?
Thanks Robert,Well I tried your suggestions and had no luck. I was running the 11.6.27 build not the RC. I just found that if I added the -s option to the command line before my script filename it works as expected. Thanks anyways. Sam Bryfczynski Computer Science Clemson University On Fri, Jul 17, 2009 at 6:52 PM, Robert Hanson wrote: > Jmol 11.8.RC3 reports: > > C:\temp>java -jar jmol.jar -x t.spt > splash_image=jar:... > history file is C:\hansonr\.jmol\history > (C) 2009 Jmol Development > Jmol Version 11.7.46 2009-06-25 18:30 > java.vendor:Sun Microsystems Inc. > java.version:1.6.0_12 > os.name:Windows XP > memory:5.5/7.0 > useCommandThread: false > User macros dir: C:\hansonr\.jmol\macros >exists: false > isDirectory: false > Executing script: ;exitJmol // Jmol -x > > C:\temp> > > Or > > C:\temp>java -jar jmol.jar -dx t.spt > splash_image=jar:file... > history file is ... > Viewer constructor org.jmol.viewer.vie...@601bb1 > (C) 2009 Jmol Development > Jmol Version 11.7.46 2009-06-25 18:30 > java.vendor:Sun Microsystems Inc. > java.version:1.6.0_12 > os.name:Windows XP > memory:5.8/6.8 > useCommandThread: false > Memory: Total-Free=3908280; Total=7499776; Free=3591496; Max=66650112 > User macros dir: ... >exists: false > isDirectory: false > 1 scripts; added: script "t.spt" > Executing script: ;exitJmol // Jmol -x > 2 scripts; added: ;exitJmol // Jmol -x > Queue[0][1] scripts; running: script "t.spt" > FileManager opening t.spt > > C:\jmol-dev\workspace\Jmol\bobtest> > > > In both cases, the script exited properly. > > Bob > > > On Fri, Jul 17, 2009 at 5:40 PM, Robert Hanson wrote: > >> Definitely a bug. What version of Jmol are you using? also try that with >> the -d option included (for "debug") >> >> >> On Fri, Jul 17, 2009 at 1:35 PM, Sam Bryfczynski wrote: >> >>> I'm trying to use jMol's ability to generate isosurface data and compress >>> it into their special file format. I need to do this through the command >>> line. The documentation says I can use the -x or -n command line options to >>> exit jMol once a script has completed. However, this does not seem to be >>> the case. All the other options seem to be ok but when I try to execute my >>> script with "java -jar jmol.jar -x myscript.spt" the script executes as it >>> should but the window remains open. I have tried this on Vista and XP >>> machines and tried many combinations of options but no luck. Please >>> help.Thanks, >>> >>> >>> Sam Bryfczynski >>> Computer Science >>> Clemson University >>> >>> >>> -- >>> Enter the BlackBerry Developer Challenge >>> This is your chance to win up to $100,000 in prizes! For a limited time, >>> vendors submitting new applications to BlackBerry App World(TM) will have >>> the opportunity to enter the BlackBerry Developer Challenge. See full >>> prize >>> details at: http://p.sf.net/sfu/Challenge >>> ___ >>> Jmol-users mailing list >>> Jmol-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> 1520 St. Olaf Ave. >> Northfield, MN 55057 >> http://www.stolaf.edu/people/hansonr >> phone: 507-786-3107 >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > -- > Enter the BlackBerry Developer Challenge > This is your chance to win up to $100,000 in prizes! For a limited time, > vendors submitting new applications to BlackBerry App World(TM) will have > the opportunity to enter the BlackBerry Developer Challenge. See full prize > details at: http://p.sf.net/sfu/Challenge > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge
Re: [Jmol-users] Third Release Candidate for Jmol 11.8
Thanks very much, Egon. I'm looking forward to showing this off at the GRC conference next week. On Fri, Jul 17, 2009 at 1:00 PM, Egon Willighagen < egon.willigha...@gmail.com> wrote: > Hi all, > > I just uploaded Release Candidate 3 for Jmol 11.8 with the following > changes: > > # code: more efficient VRML export > # new feature: set helixStep 1,2,3,... sets step for quaternion-based > analysis of structure -- see 1C4D > # bug fix: 1C4D has [FOR] -- not accepted > # bug fix: color isosurface red translucent prior to isosurface command > causes null pointer exception > # new feature: isosurface select() SET n > where n is an integer 1,2,3... that selects which set is to be displayed > and counted for area or volume > # bug fix: spacegroup reading when center of molecule is not in unit cell > can cause bonding errors > # new feature: isosurface area for subsets -- use > isosurface area select(oxygen) sasurface colorscheme sets > # bug fix: draw OFF in state script is not selective > > Have a nice weekend! > > Egon > > > -- > Post-doc @ Uppsala University > http://chem-bla-ics.blogspot.com/ > > > -- > Enter the BlackBerry Developer Challenge > This is your chance to win up to $100,000 in prizes! For a limited time, > vendors submitting new applications to BlackBerry App World(TM) will have > the opportunity to enter the BlackBerry Developer Challenge. See full prize > details at: http://p.sf.net/sfu/Challenge > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Command Line Bug?
Jmol 11.8.RC3 reports: C:\temp>java -jar jmol.jar -x t.spt splash_image=jar:... history file is C:\hansonr\.jmol\history (C) 2009 Jmol Development Jmol Version 11.7.46 2009-06-25 18:30 java.vendor:Sun Microsystems Inc. java.version:1.6.0_12 os.name:Windows XP memory:5.5/7.0 useCommandThread: false User macros dir: C:\hansonr\.jmol\macros exists: false isDirectory: false Executing script: ;exitJmol // Jmol -x C:\temp> Or C:\temp>java -jar jmol.jar -dx t.spt splash_image=jar:file... history file is ... Viewer constructor org.jmol.viewer.vie...@601bb1 (C) 2009 Jmol Development Jmol Version 11.7.46 2009-06-25 18:30 java.vendor:Sun Microsystems Inc. java.version:1.6.0_12 os.name:Windows XP memory:5.8/6.8 useCommandThread: false Memory: Total-Free=3908280; Total=7499776; Free=3591496; Max=66650112 User macros dir: ... exists: false isDirectory: false 1 scripts; added: script "t.spt" Executing script: ;exitJmol // Jmol -x 2 scripts; added: ;exitJmol // Jmol -x Queue[0][1] scripts; running: script "t.spt" FileManager opening t.spt C:\jmol-dev\workspace\Jmol\bobtest> In both cases, the script exited properly. Bob On Fri, Jul 17, 2009 at 5:40 PM, Robert Hanson wrote: > Definitely a bug. What version of Jmol are you using? also try that with > the -d option included (for "debug") > > > On Fri, Jul 17, 2009 at 1:35 PM, Sam Bryfczynski wrote: > >> I'm trying to use jMol's ability to generate isosurface data and compress >> it into their special file format. I need to do this through the command >> line. The documentation says I can use the -x or -n command line options to >> exit jMol once a script has completed. However, this does not seem to be >> the case. All the other options seem to be ok but when I try to execute my >> script with "java -jar jmol.jar -x myscript.spt" the script executes as it >> should but the window remains open. I have tried this on Vista and XP >> machines and tried many combinations of options but no luck. Please >> help.Thanks, >> >> >> Sam Bryfczynski >> Computer Science >> Clemson University >> >> >> -- >> Enter the BlackBerry Developer Challenge >> This is your chance to win up to $100,000 in prizes! For a limited time, >> vendors submitting new applications to BlackBerry App World(TM) will have >> the opportunity to enter the BlackBerry Developer Challenge. See full >> prize >> details at: http://p.sf.net/sfu/Challenge >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Command Line Bug?
Definitely a bug. What version of Jmol are you using? also try that with the -d option included (for "debug") On Fri, Jul 17, 2009 at 1:35 PM, Sam Bryfczynski wrote: > I'm trying to use jMol's ability to generate isosurface data and compress > it into their special file format. I need to do this through the command > line. The documentation says I can use the -x or -n command line options to > exit jMol once a script has completed. However, this does not seem to be > the case. All the other options seem to be ok but when I try to execute my > script with "java -jar jmol.jar -x myscript.spt" the script executes as it > should but the window remains open. I have tried this on Vista and XP > machines and tried many combinations of options but no luck. Please > help.Thanks, > > > Sam Bryfczynski > Computer Science > Clemson University > > > -- > Enter the BlackBerry Developer Challenge > This is your chance to win up to $100,000 in prizes! For a limited time, > vendors submitting new applications to BlackBerry App World(TM) will have > the opportunity to enter the BlackBerry Developer Challenge. See full prize > details at: http://p.sf.net/sfu/Challenge > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] NBO in jmol
I'm not sure I understand why two frames are necessary. You only have one file, and you are only loading it once. I think your "frame 1.1" and "frame 1.2" do nothing. Here's what I see: $ load c:/temp/nbo.gz filter "NBO" The Resolver thinks Gaussian filtering with ;NBO; filter MOs: false for " molecular orbital coefficients " Mulliken charges found for Model 1 Molecular dipole for model 1 = (2.0E-4, 3.3087997, 1.0976) Using NBO charges for Model 1 748 natural bond orbitals read 748 molecular orbitals read in model 1 $ isosurface mo1 mo 15 mo1 created with cutoff = 0.05 ; number of isosurfaces = 1 color range -1.0 1.0; mapped data range -1.0 to 1.0 $ isosurface mo2 mo 665 mo2 created with cutoff = 0.05 ; number of isosurfaces = 2 color range -1.0 1.0; mapped data range -1.0 to 1.0 $ show frames all file["1.1"] = "c:/temp/nbo.gz" title["1.1"] = "" name["1.1"] = "E(RB+HF-LYP) = -3122.57031345 A.U." so there's only one frame. > However, in order to switch from the single orbitals to the donor/acceptor > view forth and back, I am currently reloading the molecule. > You can just say isosurface delete to get rid of the current isosurfaces and start again. Certainly no need to reload the file. -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] NBO in jmol
Dear all, thanks for your help, I got is (somehow) working now: http://sassy.formativ.net/research/nbo.html However, in order to switch from the single orbitals to the donor/acceptor view forth and back, I am currently reloading the molecule. Is there a better way of doing that instead of: load files/nbo.gz filter "NBO"; rotate z 0; spin on; zoom 90; cpk off; select *; color cpk; wireframe 0.2; spacefill off; frame 1.1; isosurface color mo15 mo 15 fill translucent 0.5; frame 1.2; isosurface color mo655 mo 655 fill translucent 0.5 (that is what happens if you are pressing one of the buttons). I was trying to somehow 'clean' the used frame (so I only see the molecule again) but that does not seem to have worked. I am sure there is a better way of doing it, or? Note that I alread had to compress my file in order to speed up the loading time. All the best from Glasgow! Jörg -- * Jörg Saßmannshausen Research Fellow University of Strathclyde Department of Pure and Applied Chemistry 295 Cathedral St. Glasgow G1 1XL email: jorg.sassmannshau...@strath.ac.uk web: http://sassy.formativ.net Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Command Line Bug?
I'm trying to use jMol's ability to generate isosurface data and compress it into their special file format. I need to do this through the command line. The documentation says I can use the -x or -n command line options to exit jMol once a script has completed. However, this does not seem to be the case. All the other options seem to be ok but when I try to execute my script with "java -jar jmol.jar -x myscript.spt" the script executes as it should but the window remains open. I have tried this on Vista and XP machines and tried many combinations of options but no luck. Please help.Thanks, Sam Bryfczynski Computer Science Clemson University -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Third Release Candidate for Jmol 11.8
Hi all, I just uploaded Release Candidate 3 for Jmol 11.8 with the following changes: # code: more efficient VRML export # new feature: set helixStep 1,2,3,... sets step for quaternion-based analysis of structure -- see 1C4D # bug fix: 1C4D has [FOR] -- not accepted # bug fix: color isosurface red translucent prior to isosurface command causes null pointer exception # new feature: isosurface select() SET n where n is an integer 1,2,3... that selects which set is to be displayed and counted for area or volume # bug fix: spacegroup reading when center of molecule is not in unit cell can cause bonding errors # new feature: isosurface area for subsets -- use isosurface area select(oxygen) sasurface colorscheme sets # bug fix: draw OFF in state script is not selective Have a nice weekend! Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] suggestion: optimisation of CPK VRML export
You are welcome -- there's more to do, but I do think it is much better cleaned up this way. Thanks for suggesting that. On Fri, Jul 17, 2009 at 11:46 AM, Ralf Stephan wrote: > Many thanks for that great work, Bob! > > > ralf > > On Jul 17, 2009, at 4:53 PM, Robert Hanson wrote: > > > OK, one last fix -- I removed all XY clipping for VRML and MAYA. The > > way it was, if an object was fully outside the screen area, it was > > being clipped. But of course this has no meaning in a VRML or MAYA > > export context. So the trick right now is to zoom in on the > > structure, do the rendering, and zoom out. We could think about > > making that automatic. Right now you have to do it yourself. > > > > I'm really glad Ralf brought this up. The VRML is starting to look > > very good, I think. I just added caching for fonts and labels. > > Realize that labels are an approximation only. > > > > Bob > > > > > > On Fri, Jul 17, 2009 at 8:29 AM, Robert Hanson > > wrote: > > Angel, I've uploaded a pretty succinct VRML exporter. It was simpler > > than I thought -- only requiring one Hashtable for all objects. Not > > exactly human readable anymore, but that's not the point, right? > > Take a look. We now have DEF/USE for appearance, sphere, and > > cylinder. I also added fillTriangle, which instantly adds quite a > > bit of capability. > > > > Ah, now, the rub. The exporters are of two types. POV-RAY outputs a > > scene in the perspective coordinates of the screen. This is to > > ensure an identical output. VRML/MAYA output regular Cartesian > > coordinates, without regard to perspective. HOWEVER, in order to do > > that, they have to untransform screen points, and that is a possible > > issue. Basically the "resolution" of the VRML output is dependent > > upon the user's screen resolution. I admit that's a design flaw. I > > notice it with traces, but that's all. So maybe there's a simple fix > > there, and we will have no problem. But it is something I'm trying > > to figure out. This is about all the time I have for this now -- I > > hope I've given you a good head start with it. Thnik about > > perspective. Jmol uses a 4x4 translation/rotation matrix that can be > > obtained using viewer.getUnscaledTransformationMatrix(), which might > > work for these purposes. > > > > > > Bob > > > > > > > > 2009/7/17 Angel Herráez > > I found some interesting software: Chisel, a VRML optimizer. > > > > It's free (PD) and written in Java. One could run any files through > > it to have them reduced. Of course, if Jmol can do it straight away, > > it's better. > > Description of the optimization methods matches what we have been > > discussing about DEF / USE. > > I've collated links and brief info into the Jmol Wiki > File formats > > > 3D Objects > VRML > > > > This has also brougth another idea: to gzip the vrml file. Some > > viewers do not recognize the recommended extension, .vrz, but do read > > the file if it is gzipped but has wrl extension. Embedding wrz files > > into web pages seems to work fine. > > So, Bob, maybe the export dialog could offer a double option? > > .wrl (plain VRML v2) or .wrz (gzipped VRML v2) > > > > I am guessing that Jmol has the gzip algorithm embedded already, does > > it not? > > > > And I think we should change the current default extension of vrml to > > be wrl which seems to be more widely supported. > > > > > > > > > -- > > Enter the BlackBerry Developer Challenge > > This is your chance to win up to $100,000 in prizes! For a limited > > time, > > vendors submitting new applications to BlackBerry App World(TM) will > > have > > the opportunity to enter the BlackBerry Developer Challenge. See > > full prize > > details at: http://p.sf.net/sfu/Challenge > > ___ > > Jmol-users mailing list > > Jmol-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > > -- > > Robert M. Hanson > > Professor of Chemistry > > St. Olaf College > > 1520 St. Olaf Ave. > > Northfield, MN 55057 > > http://www.stolaf.edu/people/hansonr > > phone: 507-786-3107 > > > > > > If nature does not answer first what we want, > > it is better to take what answer we get. > > > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > > > > > -- > > Robert M. Hanson > > Professor of Chemistry > > St. Olaf College > > 1520 St. Olaf Ave. > > Northfield, MN 55057 > > http://www.stolaf.edu/people/hansonr > > phone: 507-786-3107 > > > > > > If nature does not answer first what we want, > > it is better to take what answer we get. > > > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > -- > > Enter the BlackBerry Developer Challenge > > This is your chance to win up to $100,000 in prizes! For a limited > > time, > > vendors submitting new applications to BlackBe
Re: [Jmol-users] suggestion: optimisation of CPK VRML export
Many thanks for that great work, Bob! ralf On Jul 17, 2009, at 4:53 PM, Robert Hanson wrote: > OK, one last fix -- I removed all XY clipping for VRML and MAYA. The > way it was, if an object was fully outside the screen area, it was > being clipped. But of course this has no meaning in a VRML or MAYA > export context. So the trick right now is to zoom in on the > structure, do the rendering, and zoom out. We could think about > making that automatic. Right now you have to do it yourself. > > I'm really glad Ralf brought this up. The VRML is starting to look > very good, I think. I just added caching for fonts and labels. > Realize that labels are an approximation only. > > Bob > > > On Fri, Jul 17, 2009 at 8:29 AM, Robert Hanson > wrote: > Angel, I've uploaded a pretty succinct VRML exporter. It was simpler > than I thought -- only requiring one Hashtable for all objects. Not > exactly human readable anymore, but that's not the point, right? > Take a look. We now have DEF/USE for appearance, sphere, and > cylinder. I also added fillTriangle, which instantly adds quite a > bit of capability. > > Ah, now, the rub. The exporters are of two types. POV-RAY outputs a > scene in the perspective coordinates of the screen. This is to > ensure an identical output. VRML/MAYA output regular Cartesian > coordinates, without regard to perspective. HOWEVER, in order to do > that, they have to untransform screen points, and that is a possible > issue. Basically the "resolution" of the VRML output is dependent > upon the user's screen resolution. I admit that's a design flaw. I > notice it with traces, but that's all. So maybe there's a simple fix > there, and we will have no problem. But it is something I'm trying > to figure out. This is about all the time I have for this now -- I > hope I've given you a good head start with it. Thnik about > perspective. Jmol uses a 4x4 translation/rotation matrix that can be > obtained using viewer.getUnscaledTransformationMatrix(), which might > work for these purposes. > > > Bob > > > > 2009/7/17 Angel Herráez > I found some interesting software: Chisel, a VRML optimizer. > > It's free (PD) and written in Java. One could run any files through > it to have them reduced. Of course, if Jmol can do it straight away, > it's better. > Description of the optimization methods matches what we have been > discussing about DEF / USE. > I've collated links and brief info into the Jmol Wiki > File formats > > 3D Objects > VRML > > This has also brougth another idea: to gzip the vrml file. Some > viewers do not recognize the recommended extension, .vrz, but do read > the file if it is gzipped but has wrl extension. Embedding wrz files > into web pages seems to work fine. > So, Bob, maybe the export dialog could offer a double option? > .wrl (plain VRML v2) or .wrz (gzipped VRML v2) > > I am guessing that Jmol has the gzip algorithm embedded already, does > it not? > > And I think we should change the current default extension of vrml to > be wrl which seems to be more widely supported. > > > > -- > Enter the BlackBerry Developer Challenge > This is your chance to win up to $100,000 in prizes! For a limited > time, > vendors submitting new applications to BlackBerry App World(TM) will > have > the opportunity to enter the BlackBerry Developer Challenge. See > full prize > details at: http://p.sf.net/sfu/Challenge > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > -- > Enter the BlackBerry Developer Challenge > This is your chance to win up to $100,000 in prizes! For a limited > time, > vendors submitting new applications to BlackBerry App World(TM) will > have > the opportunity to enter the BlackBerry Developer Challenge. See > full prize > details at: > http://p.sf.net/sfu/Challenge___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users Ralf Stephan http://www.ark.in-berlin.de pu
Re: [Jmol-users] suggestion: optimisation of CPK VRML export
OK, one last fix -- I removed all XY clipping for VRML and MAYA. The way it was, if an object was fully outside the screen area, it was being clipped. But of course this has no meaning in a VRML or MAYA export context. So the trick right now is to zoom in on the structure, do the rendering, and zoom out. We could think about making that automatic. Right now you have to do it yourself. I'm really glad Ralf brought this up. The VRML is starting to look very good, I think. I just added caching for fonts and labels. Realize that labels are an approximation only. Bob On Fri, Jul 17, 2009 at 8:29 AM, Robert Hanson wrote: > Angel, I've uploaded a pretty succinct VRML exporter. It was simpler than I > thought -- only requiring one Hashtable for all objects. Not exactly human > readable anymore, but that's not the point, right? Take a look. We now have > DEF/USE for appearance, sphere, and cylinder. I also added fillTriangle, > which instantly adds quite a bit of capability. > > Ah, now, the rub. The exporters are of two types. POV-RAY outputs a scene > in the perspective coordinates of the screen. This is to ensure an identical > output. VRML/MAYA output regular Cartesian coordinates, without regard to > perspective. HOWEVER, in order to do that, they have to untransform screen > points, and that is a possible issue. Basically the "resolution" of the VRML > output is dependent upon the user's screen resolution. I admit that's a > design flaw. I notice it with traces, but that's all. So maybe there's a > simple fix there, and we will have no problem. But it is something I'm > trying to figure out. This is about all the time I have for this now -- I > hope I've given you a good head start with it. Thnik about perspective. Jmol > uses a 4x4 translation/rotation matrix that can be obtained using > viewer.getUnscaledTransformationMatrix(), which might work for these > purposes. > > > Bob > > > > 2009/7/17 Angel Herráez > >> I found some interesting software: Chisel, a VRML optimizer. >> >> It's free (PD) and written in Java. One could run any files through >> it to have them reduced. Of course, if Jmol can do it straight away, >> it's better. >> Description of the optimization methods matches what we have been >> discussing about DEF / USE. >> I've collated links and brief info into the Jmol Wiki > File formats >> > 3D Objects > VRML >> >> This has also brougth another idea: to gzip the vrml file. Some >> viewers do not recognize the recommended extension, .vrz, but do read >> the file if it is gzipped but has wrl extension. Embedding wrz files >> into web pages seems to work fine. >> So, Bob, maybe the export dialog could offer a double option? >> .wrl (plain VRML v2) or .wrz (gzipped VRML v2) >> >> I am guessing that Jmol has the gzip algorithm embedded already, does >> it not? >> >> And I think we should change the current default extension of vrml to >> be wrl which seems to be more widely supported. >> >> >> >> >> -- >> Enter the BlackBerry Developer Challenge >> This is your chance to win up to $100,000 in prizes! For a limited time, >> vendors submitting new applications to BlackBerry App World(TM) will have >> the opportunity to enter the BlackBerry Developer Challenge. See full >> prize >> details at: http://p.sf.net/sfu/Challenge >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol 11.6.27 bug fix release
Hi all, I have just uploaded Jmol 11.6.27 to SourceForge, adding these bug fixes: # bug fix: color isosurface red translucent prior to isosurface command causes null pointer exception # bug fix: save/restore state fails when isosurface UNITCELL option is given # bug fix: spacegroup reading when center of molecule is not in unit cell can cause bonding errors # bug fix: draw OFF in state script is not selective Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] suggestion: optimisation of CPK VRML export
Angel, I've uploaded a pretty succinct VRML exporter. It was simpler than I thought -- only requiring one Hashtable for all objects. Not exactly human readable anymore, but that's not the point, right? Take a look. We now have DEF/USE for appearance, sphere, and cylinder. I also added fillTriangle, which instantly adds quite a bit of capability. Ah, now, the rub. The exporters are of two types. POV-RAY outputs a scene in the perspective coordinates of the screen. This is to ensure an identical output. VRML/MAYA output regular Cartesian coordinates, without regard to perspective. HOWEVER, in order to do that, they have to untransform screen points, and that is a possible issue. Basically the "resolution" of the VRML output is dependent upon the user's screen resolution. I admit that's a design flaw. I notice it with traces, but that's all. So maybe there's a simple fix there, and we will have no problem. But it is something I'm trying to figure out. This is about all the time I have for this now -- I hope I've given you a good head start with it. Thnik about perspective. Jmol uses a 4x4 translation/rotation matrix that can be obtained using viewer.getUnscaledTransformationMatrix(), which might work for these purposes. Bob 2009/7/17 Angel Herráez > I found some interesting software: Chisel, a VRML optimizer. > It's free (PD) and written in Java. One could run any files through > it to have them reduced. Of course, if Jmol can do it straight away, > it's better. > Description of the optimization methods matches what we have been > discussing about DEF / USE. > I've collated links and brief info into the Jmol Wiki > File formats > > 3D Objects > VRML > > This has also brougth another idea: to gzip the vrml file. Some > viewers do not recognize the recommended extension, .vrz, but do read > the file if it is gzipped but has wrl extension. Embedding wrz files > into web pages seems to work fine. > So, Bob, maybe the export dialog could offer a double option? > .wrl (plain VRML v2) or .wrz (gzipped VRML v2) > > I am guessing that Jmol has the gzip algorithm embedded already, does > it not? > > And I think we should change the current default extension of vrml to > be wrl which seems to be more widely supported. > > > > > -- > Enter the BlackBerry Developer Challenge > This is your chance to win up to $100,000 in prizes! For a limited time, > vendors submitting new applications to BlackBerry App World(TM) will have > the opportunity to enter the BlackBerry Developer Challenge. See full prize > details at: http://p.sf.net/sfu/Challenge > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] suggestion: optimisation of CPK VRML export
I found some interesting software: Chisel, a VRML optimizer. It's free (PD) and written in Java. One could run any files through it to have them reduced. Of course, if Jmol can do it straight away, it's better. Description of the optimization methods matches what we have been discussing about DEF / USE. I've collated links and brief info into the Jmol Wiki > File formats > 3D Objects > VRML This has also brougth another idea: to gzip the vrml file. Some viewers do not recognize the recommended extension, .vrz, but do read the file if it is gzipped but has wrl extension. Embedding wrz files into web pages seems to work fine. So, Bob, maybe the export dialog could offer a double option? .wrl (plain VRML v2) or .wrz (gzipped VRML v2) I am guessing that Jmol has the gzip algorithm embedded already, does it not? And I think we should change the current default extension of vrml to be wrl which seems to be more widely supported. -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] suggestion: optimisation of CPK VRML export
I'm going to change what I did just a bit -- the output will be about the same, but the code will be different. I agree with Ralf that we want to DEF/USE as much as possible. The catch is that you have to add about 8 bytes: "DEF " but that seems a very small price to pay for this benefit, and it almost certainly means the VRML engine will run faster as well. Here goes... 2009/7/17 Angel Herráez > El 17 Jul 2009 a las 11:59, Ralf Stephan escribió: > > > I just see that instead of USEing materials in cylinders, > > one can even USE appearances like this: > > In fact, you can DEF and USE the whole Shape, without need for > (sub)defining appearance or material. I think that's what Bob has > just implemented. > > > > -- > Enter the BlackBerry Developer Challenge > This is your chance to win up to $100,000 in prizes! For a limited time, > vendors submitting new applications to BlackBerry App World(TM) will have > the opportunity to enter the BlackBerry Developer Challenge. See full prize > details at: http://p.sf.net/sfu/Challenge > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] suggestion: optimisation of CPK VRML export
El 17 Jul 2009 a las 11:59, Ralf Stephan escribió: > I just see that instead of USEing materials in cylinders, > one can even USE appearances like this: In fact, you can DEF and USE the whole Shape, without need for (sub)defining appearance or material. I think that's what Bob has just implemented. -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] suggestion: optimisation of CPK VRML export
I just see that instead of USEing materials in cylinders,
one can even USE appearances like this:
DEF os Shape {
geometry Sphere { radius 0.34 }
appearance DEF oa Appearance {
material DEF om Material { diffuseColor 1.0 0.050980393
0.050980393 transparency 0.0 }
}
}
and later:
Transform {
translation -2.3224998 0.113 -1.43525
rotation 0.004921757 1.3608977 -0.93259245 3.14159
children [
Shape {
geometry Cylinder { height 0.60959095 radius 0.15 }
appearance USE oa
}
]
}
with further savings.
ralf
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Re: [Jmol-users] suggestion: optimisation of CPK VRML export
Well, Bob was fast as usual and has already done most of this implementation. I'll have a look at that later this evening. Ralf wrote: > But looking at the VRML, every Sphere of a specific element is > identical. > Not knowing the code, I cannot say if this holds with every molecule, > however. The issue is that you are just doing a standard ball-and-stick model, and with only a few element types, so your perception is right. But the exporter must cope with anything that the model has. For example, I could have one of the oxygens made larger and the others made small translucent spheres. The current exporter will render the vrml model as such. > This doesn't apply to the second idea, however. If you can shove > cylinders > into spheres, without compromising the result (i.e. all is opaque) then > different cylinder lengths can be had with only a few prototypes, and > better > optimisation than the first idea above. However, if you have > transparent CPK > then this looks ugly. Right, cylinders go to the atom center, so they are all shoved into spheres. But the spheres might or not be there, depending on what rendering the user chose before exporting. > Ah, I didn't think of this. > OTOH, if the user knows she won't disable spheres, she could specify > this somewhere in Jmol to get the optimisation described. Well, yes, options in the (currently nonexistent) exporting dialog could do these tricks. Not sure how difficult that would be to implement. Let's see first what Bob has got done. -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] suggestion: optimisation of CPK VRML export
>> Second, since atoms have no individuality, >> and spheres of each element the same size and material, any sphere >> can >> be a macro. > > But atoms are individual, and each one of them can be made display > at different sizes and > colors. The Jmol exporter is reading each atom and rendering it in > VRML the same way it is > rendered in Jmol. Standard CPK size and color cannot be assumed to > be the case for all > atoms. But looking at the VRML, every Sphere of a specific element is identical. Not knowing the code, I cannot say if this holds with every molecule, however. >> There is further capacity for optimisation by discretising cylinder >> joint lengths. >> If opaqueness is a condition, cylinders could be made in only a few >> sizes > > Which sizes? Bonds are of many lengths. Can't say, I haven't done a statistical analysis of cylinder lengths. Anyway, this (discretizing) possibility would depend on a given exactness. The more exact the result, the less optimisation. This doesn't apply to the second idea, however. If you can shove cylinders into spheres, without compromising the result (i.e. all is opaque) then different cylinder lengths can be had with only a few prototypes, and better optimisation than the first idea above. However, if you have transparent CPK then this looks ugly. > I guess that the vrml file could be manipulated in some software. > Then, what would happen > if e.g. the spheres were disabled? How would the molecule look like? > I think that currently it > will display correctly as sticks (must test this). Ah, I didn't think of this. OTOH, if the user knows she won't disable spheres, she could specify this somewhere in Jmol to get the optimisation described. Ralf Stephan http://www.ark.in-berlin.de pub 1024D/C5114CB2 2009-06-07 [expires: 2011-06-06] Key fingerprint = 76AE 0D21 C06C CBF9 24F8 7835 1809 DE97 C511 4CB2 -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
