From: Eric M. <mar...@ya...> - 2010-01-19 18:54:43
|
I have put an all new demo for electron density maps athttp://www.umass.edu/molvis/tests/jmol_edmEverything works!! (as far as I can tell ... now I need to learn more from the crystallographers here before I can take it further). As for the default sigma value for the contours, I have talked to 3 crystallographers. One fits at 1.0 sigma, one at 1.2 sigma, and one at 1.5 sigma. You can see the comparison between 1.0 and 1.5 at the above demo page. PyMOL offers a menu with 1.0, 2.0, and 3.0 and higher sigma. The higher values are probably used for difference maps, not for full maps. So when the cutoff value is not specified, I think Jmol should default to 1.0 sigma. I left my tests 1, 2, 3, and 4 up, but each index.html has a prominent note at the top with a link to the newest update. I found no bugs in Jmol! Kudos to Bob!! (Well, there is one minor one: after executing a jmolLink(), Jmol temporarily responds to mouse dragging with zoom -- everywhere in Jmol, not just on the right edge.) -Eric |
From: Robert H. <ha...@st...> - 2010-01-19 19:08:21
|
Great to hear that, Eric. I would be very interested in seeing on that last page a comparison of loading the ccp4 file and a JVXL version of it. Main question is: "What's a sigma?" On Tue, Jan 19, 2010 at 12:54 PM, Eric Martz <mar...@ya...> wrote: > I have put an all new demo for electron density maps at > http://www.umass.edu/molvis/tests/jmol_edm > Everything works!! (as far as I can tell ... now I need to learn more from > the crystallographers here before I can take it further). > > As for the default sigma value for the contours, I have talked to 3 > crystallographers. One fits at 1.0 sigma, one at 1.2 sigma, and one at 1.5 > sigma. You can see the comparison between 1.0 and 1.5 at the above demo > page. PyMOL offers a menu with 1.0, 2.0, and 3.0 and higher sigma. The > higher values are probably used for difference maps, not for full maps. So > when the cutoff value is not specified, I think Jmol should default to 1.0 > sigma. > > I left my tests 1, 2, 3, and 4 up, but each index.html has a prominent note > at the top with a link to the newest update. > > I found no bugs in Jmol! Kudos to Bob!! (Well, there is one minor one: > after executing a jmolLink(), Jmol temporarily responds to mouse dragging > with zoom -- everywhere in Jmol, not just on the right edge.) > > -Eric > > > > ------------------------------------------------------------------------------ > Throughout its 18-year history, RSA Conference consistently attracts the > world's best and brightest in the field, creating opportunities for > Conference > attendees to learn about information security's most important issues > through > interactions with peers, luminaries and emerging and established companies. > http://p.sf.net/sfu/rsaconf-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > 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 |
From: Eric M. <mar...@ya...> - 2010-01-19 20:16:40
|
--- On Tue, 1/19/10, Robert Hanson <ha...@st...> wrote: From: Robert Hanson <ha...@st...> Subject: Re: [Jmol-users] Electron Density Map Demo To: jmo...@li... Date: Tuesday, January 19, 2010, 2:08 PM Great to hear that, Eric. I would be very interested in seeing on that last page a comparison of loading the ccp4 file and a JVXL version of it. ERIC REPLIES:Please explain to me how to save/load the jvxl version. I wonder if that will mess up the cutoff? Why not just gzip the .ccp4 file? I haven't tried that yet but I assume it will work and cut down on file size. BOB SAID: Main question is: "What's a sigma?" ERIC REPLIEs:I wish I were prepared to answer that :-) Maybe I can find out here at the Israel Structural Proteomics Center. |
From: Robert H. <ha...@st...> - 2010-01-19 20:38:19
|
Eric, ah, so this IS something you haven't started using. No better time than now. You will really like this. The command, after displaying the isosurface, is write "3hyd.jvxl" (from the application or signed applet) then isosurface color yellow "3hyd.jvxl" mesh nofill will call it up. It will look exactly like the one you had, but the file size will be about 30-300 times smaller. (14K vs. 750K in this small protein case. The 1blu case is 60K for the JVXL file; 1.2Mb for the ccp4 file) and the loading time should be reduced substantially. You could certainly try gzipping it. But the JVXL file will still load far faster, because it doesn't have to do the grid construction that the other requires. I think pymol is just using the file values themselves for its cutoff. Bob On Tue, Jan 19, 2010 at 2:16 PM, Eric Martz <mar...@ya...> wrote: > --- On *Tue, 1/19/10, Robert Hanson <ha...@st...>* wrote: > > From: Robert Hanson <ha...@st...> > > Subject: Re: [Jmol-users] Electron Density Map Demo > To: jmo...@li... > Date: Tuesday, January 19, 2010, 2:08 PM > > > Great to hear that, Eric. I would be very interested in seeing on that > last page a comparison of loading the ccp4 file and a JVXL version of it. > > ERIC REPLIES: > Please explain to me how to save/load the jvxl version. I wonder if that > will mess up the cutoff? Why not just gzip the .ccp4 file? I haven't tried > that yet but I assume it will work and cut down on file size. > > BOB SAID: > Main question is: "What's a sigma?" > > ERIC REPLIEs: > I wish I were prepared to answer that :-) Maybe I can find out here at the > Israel Structural Proteomics Center. > > > > > ------------------------------------------------------------------------------ > Throughout its 18-year history, RSA Conference consistently attracts the > world's best and brightest in the field, creating opportunities for > Conference > attendees to learn about information security's most important issues > through > interactions with peers, luminaries and emerging and established companies. > http://p.sf.net/sfu/rsaconf-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > 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 |
From: Angel H. <ang...@ua...> - 2010-01-19 21:05:22
|
> write "3hyd.jvxl" > > (from the application or signed applet) Or pop-up menu > File > Save JVXL Isosurface with a nice Save As dialog that lets you see/choose where it is going :-) |
From: <rg...@el...> - 2010-01-19 19:27:09
|
The "sigma" is the esd (estimated standard deviation) for the value of the electron density at any grid point. So if the electron density calculations provide an esd of 1.2 electrons per cubic angstrom the 1 sigma contour lines would be at 1.2, the 2 sigma lines at 2.4, 3 sigma at 3.6 etc. Rich On Tue, 19 Jan 2010 13:08:10 -0600, Robert Hanson <ha...@st...> wrote: > Great to hear that, Eric. I would be very interested in seeing on that > last > page a comparison of loading the ccp4 file and a JVXL version of it. > > Main question is: "What's a sigma?" > > On Tue, Jan 19, 2010 at 12:54 PM, Eric Martz <mar...@ya...> wrote: > >> I have put an all new demo for electron density maps at >> http://www.umass.edu/molvis/tests/jmol_edm >> Everything works!! (as far as I can tell ... now I need to learn more >> from >> the crystallographers here before I can take it further). >> >> As for the default sigma value for the contours, I have talked to 3 >> crystallographers. One fits at 1.0 sigma, one at 1.2 sigma, and one at >> 1.5 >> sigma. You can see the comparison between 1.0 and 1.5 at the above demo >> page. PyMOL offers a menu with 1.0, 2.0, and 3.0 and higher sigma. The >> higher values are probably used for difference maps, not for full maps. >> So >> when the cutoff value is not specified, I think Jmol should default to >> 1.0 >> sigma. [snip] |
From: Brian M. <mol...@gm...> - 2010-01-19 20:02:44
|
Talk about timing, I'm sitting at my desk reading a paper where they used the term and was JUST about to go look it up. You all are incredible! - brian -----Original Message----- From: rg...@el... [mailto:rg...@el...] Sent: Tuesday, January 19, 2010 2:27 PM To: jmo...@li... Subject: Re: [Jmol-users] Electron Density Map Demo The "sigma" is the esd (estimated standard deviation) for the value of the electron density at any grid point. So if the electron density calculations provide an esd of 1.2 electrons per cubic angstrom the 1 sigma contour lines would be at 1.2, the 2 sigma lines at 2.4, 3 sigma at 3.6 etc. Rich On Tue, 19 Jan 2010 13:08:10 -0600, Robert Hanson <ha...@st...> wrote: > Great to hear that, Eric. I would be very interested in seeing on that > last > page a comparison of loading the ccp4 file and a JVXL version of it. > > Main question is: "What's a sigma?" > > On Tue, Jan 19, 2010 at 12:54 PM, Eric Martz <mar...@ya...> wrote: > >> I have put an all new demo for electron density maps at >> http://www.umass.edu/molvis/tests/jmol_edm >> Everything works!! (as far as I can tell ... now I need to learn more >> from >> the crystallographers here before I can take it further). >> >> As for the default sigma value for the contours, I have talked to 3 >> crystallographers. One fits at 1.0 sigma, one at 1.2 sigma, and one at >> 1.5 >> sigma. You can see the comparison between 1.0 and 1.5 at the above demo >> page. PyMOL offers a menu with 1.0, 2.0, and 3.0 and higher sigma. The >> higher values are probably used for difference maps, not for full maps. >> So >> when the cutoff value is not specified, I think Jmol should default to >> 1.0 >> sigma. [snip] ---------------------------------------------------------------------------- -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev _______________________________________________ Jmol-users mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-users No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.5.432 / Virus Database: 270.14.150/2632 - Release Date: 01/19/10 07:34:00 |
From: Robert H. <ha...@st...> - 2010-01-19 20:03:40
|
Is that in the file somewhere? What I have is dmin dmax dmean (density min max mean) rms Now, I DON'T think the "rms" is really "rms" -- I think it's rms deviation, but I could be wrong about that. What seems to work as a reasonable default is dmean + 2*rms But that could be a complete misuse of the numbers. OK, Brian -- we want an answer from you, then! How do we do this? :) On Tue, Jan 19, 2010 at 1:26 PM, <rg...@el...> wrote: > The "sigma" is the esd (estimated standard deviation) for the value of the > electron density at any grid point. So if the electron density calculations > provide an esd of 1.2 electrons per cubic angstrom the 1 sigma contour > lines would be at 1.2, the 2 sigma lines at 2.4, 3 sigma at 3.6 etc. > > Rich > > On Tue, 19 Jan 2010 13:08:10 -0600, Robert Hanson <ha...@st...> > wrote: > > Great to hear that, Eric. I would be very interested in seeing on that > > last > > page a comparison of loading the ccp4 file and a JVXL version of it. > > > > Main question is: "What's a sigma?" > > > > On Tue, Jan 19, 2010 at 12:54 PM, Eric Martz <mar...@ya...> > wrote: > > > >> I have put an all new demo for electron density maps at > >> http://www.umass.edu/molvis/tests/jmol_edm > >> Everything works!! (as far as I can tell ... now I need to learn more > >> from > >> the crystallographers here before I can take it further). > >> > >> As for the default sigma value for the contours, I have talked to 3 > >> crystallographers. One fits at 1.0 sigma, one at 1.2 sigma, and one at > >> 1.5 > >> sigma. You can see the comparison between 1.0 and 1.5 at the above demo > >> page. PyMOL offers a menu with 1.0, 2.0, and 3.0 and higher sigma. The > >> higher values are probably used for difference maps, not for full maps. > >> So > >> when the cutoff value is not specified, I think Jmol should default to > >> 1.0 > >> sigma. > [snip] > > > ------------------------------------------------------------------------------ > Throughout its 18-year history, RSA Conference consistently attracts the > world's best and brightest in the field, creating opportunities for > Conference > attendees to learn about information security's most important issues > through > interactions with peers, luminaries and emerging and established companies. > http://p.sf.net/sfu/rsaconf-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > 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 |
From: <rg...@el...> - 2010-01-19 20:23:38
|
On Tue, 19 Jan 2010 14:03:32 -0600, Robert Hanson <ha...@st...> wrote: > Is that in the file somewhere? What I have is > > dmin dmax dmean (density min max mean) > > rms > > Now, I DON'T think the "rms" is really "rms" -- I think it's rms deviation, > but I could be wrong about that. What seems to work as a reasonable default > is > > dmean + 2*rms > > But that could be a complete misuse of the numbers. > > OK, Brian -- we want an answer from you, then! How do we do this? :) > 1 sigma = 1 esd = 1 rmsd*rmsd i.e. the rmsd is the square root of the esd so to contour the map at 2.5 sigma: square the rmsd and multiply by 2.5 and plot lines from dmin to dmax at that interval. Rich |
From: Robert H. <ha...@st...> - 2010-01-19 21:19:31
|
Keep talking, Rich. I don't quite have it. I have a file of numbers. An isosurface is produced not by contouring but by finding the surface that intersects that cube of numbers at a specific "cutoff" value. > dmin dmax dmean (density min max mean) > > > > rms > >1 sigma = 1 esd = 1 rmsd*rmsd > > esd is what? Sorry, I really need this from the beginning. Is that the value I read from the file? What I'd like to know is what the "rms" in the file is referring to: FileManager opening 3hyd_map.ccp4 MRC header: dmin,dmax,dmean: -1.1890318,4.998787,-0.014114891 MRC header: rms: 0.74718976 Is that really the square root of the average of the squares of the numbers? I guess it could be.... FileManager opening 1blu.ccp4 MRC header: dmin,dmax,dmean: -2.0043933,4.9972544,-0.0151823275 MRC header: rms: 0.46335652 FileManager opening mrc.map MRC header: dmin,dmax,dmean: -144.45335,251.23714,2.3224847 MRC header: rms: 24.480686 FileManager opening mrc2.map MRC header: dmin,dmax,dmean: 0.0,1.0,0.34194112 MRC header: rms: 0.099831074 As you can see, these number are all over the map. As I said, my current hack of cutoff = dmean + 2 * rms seems to work acceptably, but I would like to do whatever people think really should be done. We need some sort of default, of course, and it obviously can't be a specific number. So I'm hoping that this "sigma" business is identifiable from dmean and/or rms. I note that when I have Jmol calculate the rms as sqrt ( SUM(x^2) / n ) and the rms deviation as sqrt ((sum(x^2) - mean^2)/n) I do NOT get this number..... Bob > i.e. the rmsd is the square root of the esd > > so to contour the map at 2.5 sigma: square the rmsd and multiply by 2.5 > and plot lines from dmin to dmax at that interval. > > Rich > > > ------------------------------------------------------------------------------ > Throughout its 18-year history, RSA Conference consistently attracts the > world's best and brightest in the field, creating opportunities for > Conference > attendees to learn about information security's most important issues > through > interactions with peers, luminaries and emerging and established companies. > http://p.sf.net/sfu/rsaconf-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > 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 |
From: rgb <rg...@el...> - 2010-01-19 23:59:31
|
Robert Hanson wrote: > Keep talking, Rich. I don't quite have it. > > I have a file of numbers. An isosurface is produced not by contouring > but by finding the surface that intersects that cube of numbers at a > specific "cutoff" value. > > > dmin dmax dmean (density min max mean) > > > > rms > > > >1 sigma = 1 esd = 1 rmsd*rmsd > > > esd is what? Sorry, I really need this from the beginning. Is that the > value I read from the file? > > What I'd like to know is what the "rms" in the file is referring to: > > FileManager opening 3hyd_map.ccp4 > MRC header: dmin,dmax,dmean: -1.1890318,4.998787,-0.014114891 > MRC header: rms: 0.74718976 > > Is that really the square root of the average of the squares of the > numbers? I guess it could be.... The rmsd isn't calculated from the dmin/dmax values but comes from a separate calculation which generates the map itself. When calculating the electron density value an associated calculation determines the likely error in that value and that error is the estimated standard deviation (errors are assumed to be distributed following a normal distribution curve). The rmsd value is simply the square root of the esd value. So for a point in the cell the calculation of the electron density might be, say, 3 electrons per cubic angstrom. To a crystallographer this number means more if the error associated with it is also known. So an additional calculation is run which will give a best guess for the error in those map values. Say that is 0.78 electrons. Thus for any value of the electron density we have an estimated error (standard deviation) of plus or minus 0.78 electrons. For the example you site above: the max. electron density in the map volume is 4.9988 e/A^3 with an rmsd of 0.747. Or to express it as an esd (i.e. sigma): 5.0 e/A^3 +/- 0.6 (the square of 0.747). Similarly, the minimum density is -1.2 e/A^3 +/- 0.6. I'm not sure how you want to generate the isosurface but if you are just giving it a single cutoff value then use 0.6 as a 1 sigma cutoff isosurface or 1.2 for a two sigma cutoff isosurface, etc. Rich |
From: Robert H. <ha...@st...> - 2010-01-20 02:05:36
|
Thanks, that really helps. Unfortunately, that won't work. I don't know if it's just different fields using the same data files, but the files I have that are from electron diffraction simply display nothing when you use that cutoff. Still, it might be useful to implement something like a sigma option then at least. Bob The rmsd isn't calculated from the dmin/dmax values but comes from a > separate calculation which generates the map itself. > > When calculating the electron density value an associated calculation > determines the likely error in that value and that error is the > estimated standard deviation (errors are assumed to be distributed > following a normal distribution curve). The rmsd value is simply the > square root of the esd value. > > So for a point in the cell the calculation of the electron density might > be, say, 3 electrons per cubic angstrom. To a crystallographer this > number means more if the error associated with it is also known. So an > additional calculation is run which will give a best guess for the error > in those map values. Say that is 0.78 electrons. Thus for any value of > the electron density we have an estimated error (standard deviation) of > plus or minus 0.78 electrons. > > For the example you site above: the max. electron density in the map > volume is 4.9988 e/A^3 with an rmsd of 0.747. Or to express it as an esd > (i.e. sigma): 5.0 e/A^3 +/- 0.6 (the square of 0.747). Similarly, the > minimum density is -1.2 e/A^3 +/- 0.6. > > I'm not sure how you want to generate the isosurface but if you are just > giving it a single cutoff value then use 0.6 as a 1 sigma cutoff > isosurface or 1.2 for a two sigma cutoff isosurface, etc. > > Rich > > > > > ------------------------------------------------------------------------------ > Throughout its 18-year history, RSA Conference consistently attracts the > world's best and brightest in the field, creating opportunities for > Conference > attendees to learn about information security's most important issues > through > interactions with peers, luminaries and emerging and established companies. > http://p.sf.net/sfu/rsaconf-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > 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 |
From: Grossman, R. B <rob...@uk...> - 2010-01-20 21:27:57
|
Hi, I have a JVXL file containing MO data that I am trying to display. I can see the molecule, but I can't see the MO. I have tried various scripts to turn on the MO, to no avail. Below I have copied the relevant part of my Web page. I am using 'mo HOMO;' as the script, but I have tried several other commands, including none, to no avail. How do I display the MO? Does the fact that I load inline prevent the MO from being displayed? -- Bob <script type="text/javascript"> // <!-- function getMol() { return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15 2008-11-24 13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028, -4.170638, -6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type: ?\n-32 -4.286028 -4.170638 -6.45537 ANGSTROMS\n80 0.12402356 0.0 0.0\n80 0.0 0.184445 0.0\n80 0.0 0.0 0.1257623\n6 6.0 0.0 0.0 0.0\n6 6.0 1.5335295 0.0 0.0\n8 8.0 2.3333447 1.1734227 0.0\n6 6.0 2.3022442 2.08224 -1.0298198\n6 6.0 1.9440373 3.352165 -0.783915\n6 6.0 2.166842 4.391685 -1.8063345\n8 8.0 1.4540279 5.5320063 -1.5695299\n6 6.0 1.4419276 6.5410266 -2.576349\n6 6.0 0.4292079 7.5804462 -2.13194\n1 1.0 0.699213 8.036855 -1.1707217\n1 1.0 0.36370665 8.384962 -2.8751543\n1 1.0 -0.57431144 7.149238 -2.0169382\n1 1.0 2.4541469 6.9775352 -2.6722505\n1 1.0 1.1674224 6.103718 -3.555268\n8 8.0 2.9358563 4.365084 -2.7551525\n1 1.0 1.4746284 3.6545703 0.16250335\n1 1.0 2.660351 1.708333 -1.9975383\n6 6.0 2.025939 -0.95221835 -1.101621\n1 1.0 1.6514318 -1.9706379 -0.937718\n1 1.0 1.6784323 -0.62881225 -2.0926402\n1 1.0 3.1216602 -1.0091194 -1.1394216\n1 1.0 1.869836 -0.3798073 0.9982192\n6 6.0 -0.86121655 0.62561214 -1.0898211\n6 6.0 -0.8380163 2.0938404 -1.2457241\n6 6.0 -0.81681573 2.6353507 -2.5209484\n7 7.0 -0.79011524 3.084059 -3.6053698\n6 6.0 -1.1576223 2.898656 -0.16150327\n7 7.0 -1.4360279 3.5764692 0.75561434\n1 1.0 -0.59091145 0.1594031 -2.0609396\n1 1.0 -1.9027367 0.2891056 -0.885317\n1 1.0 -0.29010567 -1.0688207 0.08750176\n1 1.0 -0.314506 0.47200906 0.95541835\n-1 35 90 35 90 Jmol voxel format version 1.4\n# \n0.05 361 -1362 1362 -1.0 1.0 -1.0 1.0 rendering:isosurface ID "homop" fill noMesh noDots notFrontOnly frontlit\n 117879 5 75 6 74 5 6154 7 72 9 71 9 71 9 72 7 75 3 5915 7 72 9 70 11 69 11 69 11 70 10 71 7 5834 4 74 9 70 11 68 13 67 13 67 13 68 12 69 9 73 5 5754 7 71 11 68 13 67 13 66 14 67 13 67 13 68 11 71 7 5752 8 71 11 68 13 66 14 66 15 65 15 66 13 68 11 71 7 334 2 77 4 77 2 5256 8 70 12 68 13 66 14 66 14 66 14 67 13 68 11 71 7 173 3 75 6 74 7 72 8 73 6 75 4 5176 8 71 11 68 12 67 14 66 14 66 14 67 12 69 10 73 4 173 6 73 8 71 10 70 9 72 8 73 6 5176 6 72 10 69 11 69 12 68 12 68 11 70 9 73 5 175 2 75 7 72 9 71 10 70 10 70 9 72 7 5256 6 72 9 71 9 71 9 72 7 75 2 256 3 75 7 72 9 71 9 71 9 71 9 72 7 5993 7 72 9 71 9 71 9 71 8 74 5 5801 4 74 7 73 7 29 5 39 7 28 7 40 4 28 8 73 7 73 6 5800 5 74 7 72 9 71 9 71 9 28 4 40 7 29 5 75 5 77 1 4709 4 77 3 1008 7 72 9 70 10 70 10 71 9 72 7 75 3 4743 3 76 5 75 5 77 3 928 7 72 9 70 10 70 10 71 9 72 7 75 3 4742 4 76 5 75 5 76 4 928 6 73 8 71 10 70 10 71 9 72 7 4820 3 77 5 75 5 76 4 929 4 75 7 72 8 72 8 73 7 74 5 4822 1 78 4 76 4 77 3 1010 5 74 6 74 6 75 5 4982 2 78 2 279630\nW4?A7Kv(0Dwm)s(RKaX!S@<V0QmxtbS9C3Omxtb9B|#HVR:PQ|RBGb<HJB!-8:#vKSHeHZQ`&A0E@t&u(DQOaJ[6>OJRKgiv\'trPM+rNK_@f7ob*7GZT4@>dX!q:`TWV@aG|ga{$l{\'-v9-WUv+p2Wmuqb@[S7k>]u[Fw,*\'Lq##%$l|R-5pEO=W?69JmAOWT<W\'_XQcN[n*cJOw\'m31X,GNHDmuXy^Izv+kA2<axMh_lP:ZqF1*-<!,lA;p.)w*)E8BQXQleUe,Z60]N<rx[zeCzs(b;23c`]buFGwJ6\/3CgjDQ@a`Tv&vjk4dj4:,+eS\'c\'e5j-mMYzUS>YS*ES9Xc^Hj9!cv|wgBP74=JC\'+G^UNYIRw@kON^c:I2*w,@re<=YqVOVpfMXiEKqP2Tntyt{_e125nBUkx4btL\'&^\'tFOE{#YXCwPuT[HX|;8XXq*P]T\/O4;9TBwZPXsOS.STEk,e*rMsrUZOT^]s.d7GeQvLo8KU!4ql(*(dRZx]Gjazd_gg@G8kN@>FWtce=9e2^F<;CSlmC.(\/ErmVLLSazymkr&w+OcjfT\/H6A]^LK+v#w=Q45JQM,UG`631[smx\/9\'-\']3h\'g9{EKKwDX7t\'y#<P^baZLp4S^+DXejjbR6Qx$>R^ecZF##uk(=JOK=%x|m<)&\/K6![mrm[4>TINK2tJrk|pN0G()UDG)N#y.7cro?(3N?QDKA:5m!)>{Wl{yxfSHnw\/BcymJ!Zd-X_ma0_Za6)S46n+]z=eAp0DAbuylL+gc`E99D].iTfkcLo@LQvz)3$xJgwBo>IiI<C:WTZ;.`\/[;[%o%\/1.1$$)9S4]Yr{pXu2;@^=FxUl^Jh0rFC6VA]Ca;A3B\/u!dz%.rz7L[`=LdD2))1Dfa1ZFI8P>-e(kr-tJc;^rH%|#g$$#8O;In3.;ibxkw)h.@]LQND\/GICGPinIc!MXjn.bD(Q7Bb[=q]W1%`*45Zz!A1))0A`lWYl@%w8p$9XR,vxM.MsTf(8\'x#=YN_<];G[vysz96LWZVJ5VT.wqH^r:dd2x7N9sRHX-9[OiXX+tjb0C?EfL<44;Ll{v{jisss1NEPSN@(0HCpc4=_JFE[)u;<&K*9Qv9oKovNQxE|,dD[|bRJIReI,T8;4$\'l#T#rgBYT\'x|diBN^FGWn`HQaA9p7IrX1j:iC|*6N1>DStklvgLFUz)F,^jlfU7NFw6ixct+;6qXN0-k7RG[K733&z%HXj7W;uXGi?X@ZMpfL++N\/&\/6`j(S.tiBS;9qARHJ\/3`8GSJHQ@WKT8hpDF.\/&&*)<;_]snyS6($+?aU+OAqyi>F4bJ&|m\'R`{3YB5ahgED38-C1gBbhXS[o|]MHOap]X^q\n|~1361 \n#-------end of jvxl file data-------\n# cutoff = 0.05; pointsPerAngstrom = 8.062984; nSurfaceInts = 361; nBytesData = 3736; bicolor map\n# created using Jvxl.java\n# precision: false nColorData 1362\n# isosurface homop cutoff +0.05 mo homo fill;\n# isosurface ID "homop" fill noMesh noDots notFrontOnly frontlit\n# bytes read: 0; approximate voxel-only input\/output byte ratio: 2794:1\n'; } // --> </script> <table style="margin-left:auto; margin-right:auto;"> <tr><td class="whiteTable" style="text-align:center;"> <script type="text/javascript"> var jmolMol0 = getMol(); var bgcolor = 'white'; var height = 250; var width = 250; var addlScripts = 'mo HOMO'; </script> <!-- method for displaying Jmol, http://jmol.sourceforge.net, in a jsp page * Java variables that must be defined in the host page: * String pathToRoot * String jmolJSCmds (semicolon-separated list of commands from Jmol * Javascript library, http://jmol.sourceforge.net/jslibrary/ ) * int jmolNum * JS variables that must be defined in the host page: * string variables jmolMol0, bgcolor, * addlScripts (semicolon-separated list of Jmol scripting commands) * int variables width, height * Use <%@ include page="" %> in the host page. --> <script type="text/javascript"> // <!-- function jmolLoaded0() { jmolLoadInline(jmolMol0, '0'); jmolScript(addlScripts, '0'); } jmolInitialize('../nosession/jmol'); bgcolor = bgcolor.replace(/#/g, 'x'); // if color has format of HTML tags if (!isNaN(parseInt(bgcolor, 16))) bgcolor = 'x' + bgcolor; // if color is hexadecimal only if (bgcolor.charAt(0) == 'x') bgcolor = '[' + bgcolor + ']'; // if color is not English var jmolStartScript = 'background ' + bgcolor + '; javascript jmolLoaded0(); '; jmolApplet([width, height], jmolStartScript, '0'); // --> </script> |
From: Robert H. <ha...@st...> - 2010-01-23 22:44:33
Attachments:
t.htm
|
<script type="text/javascript"> // <!-- function getMol() { return "JVXL functionXY\n[curveXY, (0.2, 0.0, 0.0), (21.0, 0.2, 0.0, 0.0), (21.0, 0.0, 0.2, 0.0), (11.0, 0.0, 0.0, 0.4)]\n-1 0.37794524 0.0 0.0\n21 0.37794524 0.0 0.0\n21 0.0 0.37794524 0.0\n11 0.0 0.0 0.7558905\n1 1.0 0.0 0.0 0.0 //BOGUS H ATOM ADDED FOR JVXL FORMAT\n-1 35 90 35 90 Jmol voxel format version 0.9f\n# \n1.4E-45 1647 732 -1 0.0 0.0 0.0 0.0 approximate compressionRatio=0:1\n 233 9 2 9 2 9 3 8 3 8 4 7 5 6 6 5 8 3 10 1 122 10 1 10 1 10 2 9 2 9 2 9 3 8 3 8 4 7 5 6 7 4 8 3 100 10 1 10 1 10 1 10 1 10 2 9 2 9 2 9 3 8 4 7 5 6 6 5 7 4 9 2 78 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 2 9 3 8 4 7 4 7 6 5 7 4 9 2 67 10 1 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 2 9 3 8 4 7 5 6 6 5 7 4 9 2 56 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 3 8 3 8 4 7 5 6 6 5 8 3 10 1 45 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 2 9 3 8 3 8 4 7 5 6 7 4 8 3 45 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 2 9 3 8 4 7 5 6 6 5 7 4 9 2 34 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 2 9 3 8 3 8 4 7 5 6 7 4 8 3 34 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 3 8 3 8 4 7 5 6 6 5 8 3 10 1 23 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 2 9 3 8 4 7 4 7 5 6 7 4 9 2 23 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 2 9 3 8 3 8 4 7 5 6 6 5 8 3 10 1 12 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 2 9 3 8 4 7 5 6 6 5 7 4 9 2 12 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 2 9 3 8 4 7 4 7 6 5 7 4 9 2 12 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 2 9 3 8 3 8 4 7 5 6 7 4 8 3 10 1 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 3 8 3 8 4 7 5 6 6 5 8 3 10 1 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 2 9 3 8 4 7 5 6 6 5 7 4 9 2 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 2 9 3 8 4 7 4 7 6 5 7 4 9 2 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 2 9 3 8 3 8 4 7 5 6 7 4 8 3 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 1 10 2 9 2 9 2 9 3 8 3 8 4 7 5 6 6 5 8 3\neR4H/u;iwF4:PO=>PB0.dg.dQ:^!=w#{g2iCYPMZDa<g7l2p/r,u*v(x'pgU?Wb|#|+,z5x!>1VrR.@MX`fkortvx[;,5MbfqSpibO+'Nl>*<JU^ejnqtvwpdPEhRp8DOZYWKAvVoEf*%8GS!cimqsuwX,/=W|#|9@BC51jV<^y^l3DPZbhlpsuve?0fLp?Va|$|+,y3x!>1UrR.@MX`fkortvJ&,T&)FY_k^id[K%$Kj8(;IU]djnqtv/Dob8Oqa+1BKKL>8ot`@a{4v5EQ[bhmpsuHiBl;sB[be%&./|&{^A2WsU/@MX`fkortF|#|O|$|BSvZf]d`VH|'{Ji4':IT]dinqs||T+6Sw,x5;>?1/hR:]xQh3CPZaglprO+8iY+2K`Rdp>oh[`O*'Ml=)<JU^ejnq{k|S+5lSv+x5;>?1.gnR:]xHg3CPZaglpBt)oxKu*x>N^VbN`]dRFz,vHh0&9HT]dimOZ5OBd5DUVn3p{%{q9lU4,RoiG,>LV_ejbgd>c2ho>TB`{${*+x)v[i=0UrSQ.?MW`f[eV1G;e`1>HRi1vlw(vn5hSf0*PnUC+=KV^@t{?Yt{R*3?aRt'Sv4:M=>U0.ug@Q9!jw1f2CO<oz!R`o4Q,?Rexh=Z,D]ug09:YyGQ6^QP<oC<Rr,fBicJ|#~65 \n#-------end of jvxl file data-------\n"; } </script> <script type=text/javascript src=Jmol.js></script> <script type=text/javascript> function go() { jmolScript("x = javascript('getMol()');print x;isosurface inline @x") } function go2() { jmolScript("isosurface t.jvxl") } jmolApplet() </script> <a href=javascript:go()>test</a><a href=javascript:go2()>test2</a> |
From: Grossman, R. B <rob...@uk...> - 2010-01-24 00:09:07
|
Hi Bob, The information is read from an Oracle database and written into a JSP page. We have the ability to write information to files, but we want very much to avoid having to do it. We also want to avoid having to deal with multiple files to display a single molecule and its associated MOs. From my point of view, Jmol's preference for loading information from files is a real drawback. We worked around the problem by using a .mo file instead of a .jvxl file. We were able to load the .mo file inline and display its MOs without any problem. A friend gave us the proper Jmol JS commands to use to display the MOs. jmolMenu([['mo delete;','none'],['mo 3',"3"],['mo 4',"4"] ...]); . No "isosurface" commands. I don't think that we could have mangled the .jvxl information because the .mo information, which was loaded and transmitted in exactly the same way, was not mangled. But I could be wrong. So is it correct that we use "isosurface" to load MOs into Jmol, and we use "mo" to induce Jmol to display them? -- Bob On 1/23/10 5:44 PM, "Robert Hanson" <ha...@st...> wrote: Well, two things. First, you must have mangled the data some way - or at least clipping from this page doesn't work. Because the attached file did run. Second, you can only load an isosurface "inline" like that in the very latest version of Jmol. (I'm not sure it's even in the one I have up at http://chemapps.stolaf.edu) What you would need to do is (all Jmol script here) isosurface INLINE @{javascript("getMol()")} that tells Jmol to read the output of the JavaScript getMol() function as the data for the isosurface instead of reading the data from a file. Any reason you don't want to have that data in a file? -- or is this coming back from a server and you are trying to keep it all together? Sure would be simpler: isosurface "somefile.jvxl" Bob On Wed, Jan 20, 2010 at 3:27 PM, Grossman, Robert B <rob...@uk...> wrote: Hi, I have a JVXL file containing MO data that I am trying to display. I can see the molecule, but I can't see the MO. I have tried various scripts to turn on the MO, to no avail. Below I have copied the relevant part of my Web page. I am using 'mo HOMO;' as the script, but I have tried several other commands, including none, to no avail. How do I display the MO? Does the fact that I load inline prevent the MO from being displayed? -- Bob <script type="text/javascript"> // <!-- function getMol() { return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15 2008-11-24 13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028, -4.170638, -6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type: |
From: Robert H. <ha...@st...> - 2010-01-24 02:01:37
|
I think it just got mangled as being part of the email. isosurface is used to create MOs from files that are not QM files. -- surfaces. mo is used to generate the MO data directly from the basis functions. Most people these days, I think, just let Jmol read the QM file and create the MO in the browser -- no need for a server end. Are you certain you can't do that? Bob On Sat, Jan 23, 2010 at 6:08 PM, Grossman, Robert B <rob...@uk... > wrote: > Hi Bob, > > The information is read from an Oracle database and written into a JSP > page. We have the ability to write information to files, but we want very > much to avoid having to do it. We also want to avoid having to deal with > multiple files to display a single molecule and its associated MOs. From my > point of view, Jmol's preference for loading information from files is a > real drawback. > > We worked around the problem by using a .mo file instead of a .jvxl file. > We were able to load the .mo file inline and display its MOs without any > problem. A friend gave us the proper Jmol JS commands to use to display the > MOs. jmolMenu([['mo delete;','none'],['mo 3',"3"],['mo 4',"4"] ...]); . No > "isosurface" commands. > > I don't think that we could have mangled the .jvxl information because the > .mo information, which was loaded and transmitted in exactly the same way, > was not mangled. But I could be wrong. > > So is it correct that we use "isosurface" to load MOs into Jmol, and we use > "mo" to induce Jmol to display them? > > -- Bob > > On 1/23/10 5:44 PM, "Robert Hanson" <ha...@st...> wrote: > > Well, two things. First, you must have mangled the data some way - or at > least clipping from this page doesn't work. Because the attached file did > run. Second, you can only load an isosurface "inline" like that in the very > latest version of Jmol. (I'm not sure it's even in the one I have up at > http://chemapps.stolaf.edu) What you would need to do is (all Jmol script > here) > > isosurface INLINE @{javascript("getMol()")} > > that tells Jmol to read the output of the JavaScript getMol() function as > the data for the isosurface instead of reading the data from a file. > > Any reason you don't want to have that data in a file? -- or is this coming > back from a server and you are trying to keep it all together? Sure would be > simpler: > > isosurface "somefile.jvxl" > > Bob > > > > On Wed, Jan 20, 2010 at 3:27 PM, Grossman, Robert B < > rob...@uk...> wrote: > Hi, > > I have a JVXL file containing MO data that I am trying to display. I can > see the molecule, but I can't see the MO. I have tried various scripts to > turn on the MO, to no avail. Below I have copied the relevant part of my > Web page. I am using 'mo HOMO;' as the script, but I have tried several > other commands, including none, to no avail. How do I display the MO? Does > the fact that I load inline prevent the MO from being displayed? > > -- Bob > > <script type="text/javascript"> > // <!-- > function getMol() { > return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15 > 2008-11-24 13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028, > -4.170638, -6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type: > > > > > ------------------------------------------------------------------------------ > Throughout its 18-year history, RSA Conference consistently attracts the > world's best and brightest in the field, creating opportunities for > Conference > attendees to learn about information security's most important issues > through > interactions with peers, luminaries and emerging and established companies. > http://p.sf.net/sfu/rsaconf-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > 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 |
From: Grossman, R. B <rob...@uk...> - 2010-01-24 03:33:16
|
We can let Jmol create the MO from the QM data in the browser - I think that is what we are doing now with the .mo file - but we greatly prefer to read the QM data from the database, not from a file. I'm still trying to understand the mutual dependencies among load, isosurface, and mo. When I use "jmolLoadInline()" with the contents of the .mo file, I can see the structure, and I can use the script "mo" (as implemented by the jmolMenu() JS command) to display the MOs. When I use "jmolLoadInline()" with the contents of the .jvxl file, I can see the structure, but I cannot find a script that will display the isosurface. Is there a script that will display the isosurface after I load it into Jmol with "jmolLoadInline()"? On 1/23/10 8:39 PM, "Robert Hanson" <ha...@st...> wrote: I think it just got mangled as being part of the email. isosurface is used to create MOs from files that are not QM files. -- surfaces. mo is used to generate the MO data directly from the basis functions. Most people these days, I think, just let Jmol read the QM file and create the MO in the browser -- no need for a server end. Are you certain you can't do that? Bob On Sat, Jan 23, 2010 at 6:08 PM, Grossman, Robert B <rob...@uk...> wrote: Hi Bob, The information is read from an Oracle database and written into a JSP page. We have the ability to write information to files, but we want very much to avoid having to do it. We also want to avoid having to deal with multiple files to display a single molecule and its associated MOs. From my point of view, Jmol's preference for loading information from files is a real drawback. We worked around the problem by using a .mo file instead of a .jvxl file. We were able to load the .mo file inline and display its MOs without any problem. A friend gave us the proper Jmol JS commands to use to display the MOs. jmolMenu([['mo delete;','none'],['mo 3',"3"],['mo 4',"4"] ...]); . No "isosurface" commands. I don't think that we could have mangled the .jvxl information because the .mo information, which was loaded and transmitted in exactly the same way, was not mangled. But I could be wrong. So is it correct that we use "isosurface" to load MOs into Jmol, and we use "mo" to induce Jmol to display them? -- Bob On 1/23/10 5:44 PM, "Robert Hanson" <ha...@st...> wrote: Well, two things. First, you must have mangled the data some way - or at least clipping from this page doesn't work. Because the attached file did run. Second, you can only load an isosurface "inline" like that in the very latest version of Jmol. (I'm not sure it's even in the one I have up at http://chemapps.stolaf.edu) What you would need to do is (all Jmol script here) isosurface INLINE @{javascript("getMol()")} that tells Jmol to read the output of the JavaScript getMol() function as the data for the isosurface instead of reading the data from a file. Any reason you don't want to have that data in a file? -- or is this coming back from a server and you are trying to keep it all together? Sure would be simpler: isosurface "somefile.jvxl" Bob On Wed, Jan 20, 2010 at 3:27 PM, Grossman, Robert B <rob...@uk...> wrote: Hi, I have a JVXL file containing MO data that I am trying to display. I can see the molecule, but I can't see the MO. I have tried various scripts to turn on the MO, to no avail. Below I have copied the relevant part of my Web page. I am using 'mo HOMO;' as the script, but I have tried several other commands, including none, to no avail. How do I display the MO? Does the fact that I load inline prevent the MO from being displayed? -- Bob <script type="text/javascript"> // <!-- function getMol() { return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15 2008-11-24 13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028, -4.170638, -6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type: ------------------------------------------------------------------------------ Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev _______________________________________________ Jmol-users mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Robert H. <ha...@st...> - 2010-01-24 04:34:16
|
On Sat, Jan 23, 2010 at 9:33 PM, Grossman, Robert B <rob...@uk... > wrote: > We can let Jmol create the MO from the QM data in the browser - I think > that is what we are doing now with the .mo file - but we greatly prefer to > read the QM data from the database, not from a file. > > I'm still trying to understand the mutual dependencies among load, > isosurface, and mo. > > When I use "jmolLoadInline()" with the contents of the .mo file, I can see > the structure, and I can use the script "mo" (as implemented by the > jmolMenu() JS command) to display the MOs. > > By .MO file, not sure what you mean there, unless that's a WebMO file. The fact that you can use the MO command indicates that you are creating the orbitals from the basis functions and coefficients. > When I use "jmolLoadInline()" with the contents of the .jvxl file, I can > see the structure, but I cannot find a script that will display the > isosurface. Is there a script that will display the isosurface after I load > it into Jmol with "jmolLoadInline()"? > > > This older JVXL file format was modeled on the CUBE format and thus did save up to the first 100 atoms; the newer XML version doesn't. But all you are doing there is reading the atoms. The load command doesn't read any surfaces ever. If the file has QM basis and coefficients, then those are read at load time (and the popup menu will be populated with items showing all the orbitals and their energies). The JVXL file is really a surface file and is read using the ISOSURFACE command. Until last week you couldn't load those inline. (You could load PMESH data -- simple triangles -- inline, but you couldn't use the isosurface INLINE keyword with anything else. I think I changed that early last week. So if that's really what you want to do, you need to use Jmol 11.9.21. So you can load MO data two ways -- with the LOAD/MO command combination or with the ISOSURFACE command. In Jmol "MO" is a subset of "ISOSURFACE" so the same code is run, but the options are a bit different. When you use MO homo you get a basic, standard orbital, with a nice listing of orbital properties in the upper left corner. Options are pretty much limited to cutoff and color. With ISOSURFACE MO homo you don't get that listing, but you have a bit more flexibility -- you can, for example, choose to ignore atoms and only see contributions from a subset, and you can do contouring, planar slices, "topo" maps, and such. I need to get this into the documentation.... Bob > > On 1/23/10 8:39 PM, "Robert Hanson" <ha...@st...> wrote: > > I think it just got mangled as being part of the email. > > isosurface is used to create MOs from files that are not QM files. -- > surfaces. > mo is used to generate the MO data directly from the basis functions. Most > people these days, I think, just let Jmol read the QM file and create the MO > in the browser -- no need for a server end. Are you certain you can't do > that? > > Bob > > On Sat, Jan 23, 2010 at 6:08 PM, Grossman, Robert B < > rob...@uk...> wrote: > Hi Bob, > > The information is read from an Oracle database and written into a JSP > page. We have the ability to write information to files, but we want very > much to avoid having to do it. We also want to avoid having to deal with > multiple files to display a single molecule and its associated MOs. From my > point of view, Jmol's preference for loading information from files is a > real drawback. > > We worked around the problem by using a .mo file instead of a .jvxl file. > We were able to load the .mo file inline and display its MOs without any > problem. A friend gave us the proper Jmol JS commands to use to display the > MOs. jmolMenu([['mo delete;','none'],['mo 3',"3"],['mo 4',"4"] ...]); . No > "isosurface" commands. > > I don't think that we could have mangled the .jvxl information because the > .mo information, which was loaded and transmitted in exactly the same way, > was not mangled. But I could be wrong. > > So is it correct that we use "isosurface" to load MOs into Jmol, and we use > "mo" to induce Jmol to display them? > > -- Bob > > On 1/23/10 5:44 PM, "Robert Hanson" <ha...@st...> wrote: > > Well, two things. First, you must have mangled the data some way - or at > least clipping from this page doesn't work. Because the attached file did > run. Second, you can only load an isosurface "inline" like that in the very > latest version of Jmol. (I'm not sure it's even in the one I have up at > http://chemapps.stolaf.edu) What you would need to do is (all Jmol script > here) > > isosurface INLINE @{javascript("getMol()")} > > that tells Jmol to read the output of the JavaScript getMol() function as > the data for the isosurface instead of reading the data from a file. > > Any reason you don't want to have that data in a file? -- or is this coming > back from a server and you are trying to keep it all together? Sure would be > simpler: > > isosurface "somefile.jvxl" > > Bob > > > > On Wed, Jan 20, 2010 at 3:27 PM, Grossman, Robert B < > rob...@uk...> wrote: > Hi, > > I have a JVXL file containing MO data that I am trying to display. I can > see the molecule, but I can't see the MO. I have tried various scripts to > turn on the MO, to no avail. Below I have copied the relevant part of my > Web page. I am using 'mo HOMO;' as the script, but I have tried several > other commands, including none, to no avail. How do I display the MO? Does > the fact that I load inline prevent the MO from being displayed? > > -- Bob > > <script type="text/javascript"> > // <!-- > function getMol() { > return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15 > 2008-11-24 13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028, > -4.170638, -6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type: > > > > > ------------------------------------------------------------------------------ > Throughout its 18-year history, RSA Conference consistently attracts the > world's best and brightest in the field, creating opportunities for > Conference > attendees to learn about information security's most important issues > through > interactions with peers, luminaries and emerging and established companies. > http://p.sf.net/sfu/rsaconf-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > ------------------------------------------------------------------------------ > Throughout its 18-year history, RSA Conference consistently attracts the > world's best and brightest in the field, creating opportunities for > Conference > attendees to learn about information security's most important issues > through > interactions with peers, luminaries and emerging and established companies. > http://p.sf.net/sfu/rsaconf-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > 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 |
From: Grossman, R. B <rob...@uk...> - 2010-01-24 05:59:29
|
Ah, I see. And the .jvxl file that my friend sent me must have been created by Jmol from a QM calculation that my friend had generated with WebMO and loaded into Jmol. So when he was trying to make my life easier by sending me the .jvxl file instead of the WebMO results file, he was really making it more difficult, because I was loading the data inline, and Jmol couldn't read the isosurface data in the .jvxl file. It all becomes much clearer now... It seems the best solution for us is just to store the QM results file into the database, deliver the data inline to Jmol, and use scripts and the Javascript library to have Jmol generate the MOs. It achieves all our goals. Thanks for your patient explanations. On 1/23/10 11:34 PM, "Robert Hanson" <ha...@st...> wrote: On Sat, Jan 23, 2010 at 9:33 PM, Grossman, Robert B <rob...@uk...> wrote: We can let Jmol create the MO from the QM data in the browser - I think that is what we are doing now with the .mo file - but we greatly prefer to read the QM data from the database, not from a file. I'm still trying to understand the mutual dependencies among load, isosurface, and mo. When I use "jmolLoadInline()" with the contents of the .mo file, I can see the structure, and I can use the script "mo" (as implemented by the jmolMenu() JS command) to display the MOs. By .MO file, not sure what you mean there, unless that's a WebMO file. The fact that you can use the MO command indicates that you are creating the orbitals from the basis functions and coefficients. When I use "jmolLoadInline()" with the contents of the .jvxl file, I can see the structure, but I cannot find a script that will display the isosurface. Is there a script that will display the isosurface after I load it into Jmol with "jmolLoadInline()"? This older JVXL file format was modeled on the CUBE format and thus did save up to the first 100 atoms; the newer XML version doesn't. But all you are doing there is reading the atoms. The load command doesn't read any surfaces ever. If the file has QM basis and coefficients, then those are read at load time (and the popup menu will be populated with items showing all the orbitals and their energies). The JVXL file is really a surface file and is read using the ISOSURFACE command. Until last week you couldn't load those inline. (You could load PMESH data -- simple triangles -- inline, but you couldn't use the isosurface INLINE keyword with anything else. I think I changed that early last week. So if that's really what you want to do, you need to use Jmol 11.9.21. So you can load MO data two ways -- with the LOAD/MO command combination or with the ISOSURFACE command. In Jmol "MO" is a subset of "ISOSURFACE" so the same code is run, but the options are a bit different. When you use MO homo you get a basic, standard orbital, with a nice listing of orbital properties in the upper left corner. Options are pretty much limited to cutoff and color. With ISOSURFACE MO homo you don't get that listing, but you have a bit more flexibility -- you can, for example, choose to ignore atoms and only see contributions from a subset, and you can do contouring, planar slices, "topo" maps, and such. I need to get this into the documentation.... Bob On 1/23/10 8:39 PM, "Robert Hanson" <ha...@st...> wrote: I think it just got mangled as being part of the email. isosurface is used to create MOs from files that are not QM files. -- surfaces. mo is used to generate the MO data directly from the basis functions. Most people these days, I think, just let Jmol read the QM file and create the MO in the browser -- no need for a server end. Are you certain you can't do that? Bob On Sat, Jan 23, 2010 at 6:08 PM, Grossman, Robert B <rob...@uk...> wrote: Hi Bob, The information is read from an Oracle database and written into a JSP page. We have the ability to write information to files, but we want very much to avoid having to do it. We also want to avoid having to deal with multiple files to display a single molecule and its associated MOs. From my point of view, Jmol's preference for loading information from files is a real drawback. We worked around the problem by using a .mo file instead of a .jvxl file. We were able to load the .mo file inline and display its MOs without any problem. A friend gave us the proper Jmol JS commands to use to display the MOs. jmolMenu([['mo delete;','none'],['mo 3',"3"],['mo 4',"4"] ...]); . No "isosurface" commands. I don't think that we could have mangled the .jvxl information because the .mo information, which was loaded and transmitted in exactly the same way, was not mangled. But I could be wrong. So is it correct that we use "isosurface" to load MOs into Jmol, and we use "mo" to induce Jmol to display them? -- Bob On 1/23/10 5:44 PM, "Robert Hanson" <ha...@st...> wrote: Well, two things. First, you must have mangled the data some way - or at least clipping from this page doesn't work. Because the attached file did run. Second, you can only load an isosurface "inline" like that in the very latest version of Jmol. (I'm not sure it's even in the one I have up at http://chemapps.stolaf.edu) What you would need to do is (all Jmol script here) isosurface INLINE @{javascript("getMol()")} that tells Jmol to read the output of the JavaScript getMol() function as the data for the isosurface instead of reading the data from a file. Any reason you don't want to have that data in a file? -- or is this coming back from a server and you are trying to keep it all together? Sure would be simpler: isosurface "somefile.jvxl" Bob On Wed, Jan 20, 2010 at 3:27 PM, Grossman, Robert B <rob...@uk...> wrote: Hi, I have a JVXL file containing MO data that I am trying to display. I can see the molecule, but I can't see the MO. I have tried various scripts to turn on the MO, to no avail. Below I have copied the relevant part of my Web page. I am using 'mo HOMO;' as the script, but I have tried several other commands, including none, to no avail. How do I display the MO? Does the fact that I load inline prevent the MO from being displayed? -- Bob <script type="text/javascript"> // <!-- function getMol() { return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15 2008-11-24 13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028, -4.170638, -6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type: ------------------------------------------------------------------------------ Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev _______________________________________________ Jmol-users mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev _______________________________________________ Jmol-users mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Robert H. <ha...@st...> - 2010-01-24 10:53:14
|
Bob, I'll be very interested in seeing what you end up with. A couple more thoughts on this.... I did some tests, and there are two problems. First, the data are definitely mangled. I see escape sequences that should not be there -- \/ -- (escape FORWARD slash) for example, and there must be something else wrong, because what is happening is that the first "cryptic" line, which represents the position of the edges of the triangles, is too short, so Jmol is going to the next line (the color line, which in this case just indicates no color) and reading that. Then it runs out of data on the color line and chokes. I find no problem reading JVXL files written by 11.6.21 (I don't have 11.6.15 here) and no notes relating to bug fixes, so I think there's no problem with the ORIGINAL JVXL file. Something along the way of getting it into the database and back out has mangled it or possibly something in gmail wrecked it. I don't know. Yes, the WebMO .MO file would be FAR better to save in the database, because it preserves all the other useful information. Also, there's a bug in Jmol that doesn't let it read isosurface data from the inline string. The following WOULD be the way to read that file if that bug were not there: jmolAppletInline(300,getMol(),"isosurface '';" ) (that's isosurface single-quote single-quote) In other words, "load the model inline and then read the isosurface from the file that was loaded". That will work in the next version of Jmol. But you won't need it if you use the MO file. With that you would just use: jmolAppletInline(300,getMol(),"mo 1") and if there are multiple MOs in the file, then you can get all of them in the right-click menu, and you can enumerate them on your page using: jmolAppletInline(300,getMol(),"mo 1;javascript 'fileLoaded()'; ") and then, in JavaScript: function fileLoaded() { var mos = jmolGetPropertyAsArray("auxiliaryInfo.models[1].moData.mos") alert(mos.length + " molecular orbitals were loaded") for (var i = 0; i < mos.length; i++) { alert(mos[i].energy) } } The auxiliaryInfo property has data like this: auxiliaryinfo.models[1].moData.mos *Vector[1] auxiliaryinfo.models[1].moData.mos[1].occupancy 2.0 auxiliaryinfo.models[1].moData.mos[1].energy -0.42780003 auxiliaryinfo.models[1].moData.calculationType "?" auxiliaryinfo.models[1].moData.energyUnits "eV" [Note that in JavaScript you have to reduce those indexes by 1 because Jmol starts with [1] and goes through [0] (so you can always pick up the last element with [0] or the next to last with [-1], etc.] You have to be a little careful there, as indicated, so that you do not try to access file information until the applet is downloaded and the model file is loaded. Here's the generic way to do that that also shows how you can display all the auxiliary info that came with the file: <head> function getMol() { return "some valid model file data" } function fileLoaded() { var info = jmolGetPropertyAsString("auxiliaryInfo") document.getElementById("outputdiv").innerHTML = "<pre>" + info + "<pre>"; } </script> </head><body> <script type=text/javascript> jmolAppletInline(300,getMol(),"javascript fileLoaded()") </script> <div id="outputdiv"></div> </body> </html> My point is simply that you can easily pull out the information in the .MO file that could be useful in the web page presentation. Good luck! Bob On Sat, Jan 23, 2010 at 11:59 PM, Grossman, Robert B < rob...@uk...> wrote: > Ah, I see. And the .jvxl file that my friend sent me must have been > created by Jmol from a QM calculation that my friend had generated with > WebMO and loaded into Jmol. So when he was trying to make my life easier by > sending me the .jvxl file instead of the WebMO results file, he was really > making it more difficult, because I was loading the data inline, and Jmol > couldn't read the isosurface data in the .jvxl file. > > It all becomes much clearer now... > > It seems the best solution for us is just to store the QM results file into > the database, deliver the data inline to Jmol, and use scripts and the > Javascript library to have Jmol generate the MOs. It achieves all our > goals. > > Thanks for your patient explanations. > > > On 1/23/10 11:34 PM, "Robert Hanson" <ha...@st...> wrote: > > > > On Sat, Jan 23, 2010 at 9:33 PM, Grossman, Robert B < > rob...@uk...> wrote: > We can let Jmol create the MO from the QM data in the browser - I think > that is what we are doing now with the .mo file - but we greatly prefer to > read the QM data from the database, not from a file. > > I'm still trying to understand the mutual dependencies among load, > isosurface, and mo. > > When I use "jmolLoadInline()" with the contents of the .mo file, I can see > the structure, and I can use the script "mo" (as implemented by the > jmolMenu() JS command) to display the MOs. > > > By .MO file, not sure what you mean there, unless that's a WebMO file. The > fact that you can use the MO command indicates that you are creating the > orbitals from the basis functions and coefficients. > > When I use "jmolLoadInline()" with the contents of the .jvxl file, I can > see the structure, but I cannot find a script that will display the > isosurface. Is there a script that will display the isosurface after I load > it into Jmol with "jmolLoadInline()"? > > > > This older JVXL file format was modeled on the CUBE format and thus did > save up to the first 100 atoms; the newer XML version doesn't. But all you > are doing there is reading the atoms. The load command doesn't read any > surfaces ever. If the file has QM basis and coefficients, then those are > read at load time (and the popup menu will be populated with items showing > all the orbitals and their energies). > > The JVXL file is really a surface file and is read using the ISOSURFACE > command. Until last week you couldn't load those inline. (You could load > PMESH data -- simple triangles -- inline, but you couldn't use the > isosurface INLINE keyword with anything else. I think I changed that early > last week. So if that's really what you want to do, you need to use Jmol > 11.9.21. > > So you can load MO data two ways -- with the LOAD/MO command combination or > with the ISOSURFACE command. In Jmol "MO" is a subset of "ISOSURFACE" so the > same code is run, but the options are a bit different. When you use > > MO homo > > you get a basic, standard orbital, with a nice listing of orbital > properties in the upper left corner. Options are pretty much limited to > cutoff and color. With > > ISOSURFACE MO homo > > you don't get that listing, but you have a bit more flexibility -- you can, > for example, choose to ignore atoms and only see contributions from a > subset, and you can do contouring, planar slices, "topo" maps, and such. I > need to get this into the documentation.... > > Bob > > > > > On 1/23/10 8:39 PM, "Robert Hanson" <ha...@st...> wrote: > > I think it just got mangled as being part of the email. > > isosurface is used to create MOs from files that are not QM files. -- > surfaces. > mo is used to generate the MO data directly from the basis functions. Most > people these days, I think, just let Jmol read the QM file and create the MO > in the browser -- no need for a server end. Are you certain you can't do > that? > > Bob > > On Sat, Jan 23, 2010 at 6:08 PM, Grossman, Robert B < > rob...@uk...> wrote: > Hi Bob, > > The information is read from an Oracle database and written into a JSP > page. We have the ability to write information to files, but we want very > much to avoid having to do it. We also want to avoid having to deal with > multiple files to display a single molecule and its associated MOs. From my > point of view, Jmol's preference for loading information from files is a > real drawback. > > We worked around the problem by using a .mo file instead of a .jvxl file. > We were able to load the .mo file inline and display its MOs without any > problem. A friend gave us the proper Jmol JS commands to use to display the > MOs. jmolMenu([['mo delete;','none'],['mo 3',"3"],['mo 4',"4"] ...]); . No > "isosurface" commands. > > I don't think that we could have mangled the .jvxl information because the > .mo information, which was loaded and transmitted in exactly the same way, > was not mangled. But I could be wrong. > > So is it correct that we use "isosurface" to load MOs into Jmol, and we use > "mo" to induce Jmol to display them? > > -- Bob > > On 1/23/10 5:44 PM, "Robert Hanson" <ha...@st...> wrote: > > Well, two things. First, you must have mangled the data some way - or at > least clipping from this page doesn't work. Because the attached file did > run. Second, you can only load an isosurface "inline" like that in the very > latest version of Jmol. (I'm not sure it's even in the one I have up at > http://chemapps.stolaf.edu) What you would need to do is (all Jmol script > here) > > isosurface INLINE @{javascript("getMol()")} > > that tells Jmol to read the output of the JavaScript getMol() function as > the data for the isosurface instead of reading the data from a file. > > Any reason you don't want to have that data in a file? -- or is this coming > back from a server and you are trying to keep it all together? Sure would be > simpler: > > isosurface "somefile.jvxl" > > Bob > > > > On Wed, Jan 20, 2010 at 3:27 PM, Grossman, Robert B < > rob...@uk...> wrote: > Hi, > > I have a JVXL file containing MO data that I am trying to display. I can > see the molecule, but I can't see the MO. I have tried various scripts to > turn on the MO, to no avail. Below I have copied the relevant part of my > Web page. I am using 'mo HOMO;' as the script, but I have tried several > other commands, including none, to no avail. How do I display the MO? Does > the fact that I load inline prevent the MO from being displayed? > > -- Bob > > <script type="text/javascript"> > // <!-- > function getMol() { > return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15 > 2008-11-24 13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028, > -4.170638, -6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type: > > > > > ------------------------------------------------------------------------------ > Throughout its 18-year history, RSA Conference consistently attracts the > world's best and brightest in the field, creating opportunities for > Conference > attendees to learn about information security's most important issues > through > interactions with peers, luminaries and emerging and established companies. > http://p.sf.net/sfu/rsaconf-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > ------------------------------------------------------------------------------ > Throughout its 18-year history, RSA Conference consistently attracts the > world's best and brightest in the field, creating opportunities for > Conference > attendees to learn about information security's most important issues > through > interactions with peers, luminaries and emerging and established companies. > http://p.sf.net/sfu/rsaconf-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > ------------------------------------------------------------------------------ > Throughout its 18-year history, RSA Conference consistently attracts the > world's best and brightest in the field, creating opportunities for > Conference > attendees to learn about information security's most important issues > through > interactions with peers, luminaries and emerging and established companies. > http://p.sf.net/sfu/rsaconf-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > 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 |