From: Bob H. <ha...@st...> - 2006-03-16 22:35:37
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I've implemented some changes to rotate. First, all the standard stuff is unchanged. You can certainly still do rotate x 50 rotate z -10 but now there are more options. Prinipal among them: 1) You can address either the "fixed" xyz coordinate system of the Jmol window as these commands do, or you can now rotate around the "internal" model frame (the axes you see when you "set axes on". So, for example: rotate INTERNAL x 20 rotates the model around its center point about IT's x axis, regardless of how you might have rotated the molecule with respect to the fixed frame. 2) You can specify an atom or set of atoms around which you wish to rotate: rotate x 20 (atomno=3) That's a full atom expression -- anything you could select you could put in there. Or: rotate INTERNAL x 10 (oxygen) That would be about the geometric centers of all the oxygens on an axis that is parallel to the model's internal x axis. 3) You can include a second atom set; the INTERNAL keyword is now implied and unnecessary: rotate 30 (atomno=3) (atomno=5) To complement this, I've added a new picking option: SPIN. So you can say set pickingMode SPIN 20 The spin rate, 20 in this case, is optional. 10 is the default. Now when you click on two atoms, the model smoothly rotates around an invisible axis connecting them. Click again, and rotation stops. Click more, and it rotates around whatever atoms you have chosen. Tell me this isn't fun! 4) You can substitute xyz coordinates as [x,y,z] (commas optional, but brackets required. Those are internal coordinates, of course. rotate 20 [0 0 0] [1 1 1] rotate 20 x [2 2 0] 5) You can specify a previously drawn object (point, line, or plane) to use for the rotation or in place of an atom set for its center position. Brackets are required. draw line1 150 (atomno=1) (atomno=14) rotate [line1] 30 Ends of these drawn lines automatically become rotation initiators, by the way. Click on the end of any drawn line, and the model will rotate. SHIFT-click and it will go clockwise. You can set the rate with set picking spin 30 6) You can specify an axis and an angle, either FIXED or INTERNAL and rotate around it: rotate axisangle INTERNAL 20 [1 1 1] does the same as above, but rotate axisangle 20 [1 1 1] rotates in the FIXED frame instead. 7) Finally, I added "-x" "-y" and "-z" just for good measure and also gave rotate some defaults -- y axis at a rate of 10. So you can use: rotate rotate 20 rotate -x rotate -z A decent test page is at http://www.stolaf.edu/people/hansonr/jmol/test/json/spin.htm Bob Hanson -- Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein |
From: Rajarshi G. <rx...@ps...> - 2006-03-16 22:41:27
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On Thu, 2006-03-16 at 16:35 -0600, Bob Hanson wrote: > > A decent test page is at > http://www.stolaf.edu/people/hansonr/jmol/test/json/spin.htm I was trying to look at the above example page but when I click on the links nothing happens. Looking at my Javascript console I see: Error: applet.getPropertyAsJSON is not a function Source File: http://www.stolaf.edu/people/hansonr/jmol/test/json/Jmol-new.js Line: 923 and Error: applet.script is not a function Source File: http://www.stolaf.edu/people/hansonr/jmol/test/json/Jmol-new.js Line: 264 I'm running Firefox 1.0.4, JDK 1.5, Fedora Core 4. Is there something I need to install/setup? - I haven't kept up with the browser/jdk requirements for the applet :( ------------------------------------------------------------------- Rajarshi Guha <rx...@ps...> <http://jijo.cjb.net> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- All seems condemned in the long run to approximate a state akin to Gaussian noise. -- James Martin |
From: Frieda R. <fr...@ns...> - 2006-03-17 13:25:44
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On Mar 16, 2006, at 5:42 PM, Rajarshi Guha wrote: > I'm running Firefox 1.0.4, JDK 1.5, Fedora Core 4. > > Is there something I need to install/setup? - I haven't kept up > with the > browser/jdk requirements for the applet :( Hi Rajarshi, In my experience, problems with Firefox can usually be avoided by upgrading to Firefox. 1.5-- but I am not familiar with Fedora. However, it might be easiest to try that first. HTH, Frieda /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |
From: Rolf H. <rh...@fl...> - 2006-03-17 14:38:21
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Frieda Reichsman wrote: > > On Mar 16, 2006, at 5:42 PM, Rajarshi Guha wrote: >> I'm running Firefox 1.0.4, JDK 1.5, Fedora Core 4. >> >> Is there something I need to install/setup? - I haven't kept up with the >> browser/jdk requirements for the applet :( > > Hi Rajarshi, > > In my experience, problems with Firefox can usually be avoided by > upgrading to Firefox. 1.5-- but I am not familiar with Fedora. > However, it might be easiest to try that first. > HTH, > Frieda In my experience Firefox 1.5 (WindowsXP) seems to be much more unstable with Jmol (V. 10.00.36) than Firefox 1.06/1.07 (Windows XP/ Linux). Regards, Rolf |
From: Bob H. <ha...@st...> - 2006-03-17 15:02:59
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This, I believe is a browser/Live Connect problem. What is your experience with, say, the pages in http://www.stolaf.edu/people/hansonr/jmol/docs/examples or the pop-up windows from http://www.stolaf.edu/people/hansonr/jmol/docs ? Rajarshi Guha wrote: > On Thu, 2006-03-16 at 16:35 -0600, Bob Hanson wrote: > > >>A decent test page is at >>http://www.stolaf.edu/people/hansonr/jmol/test/json/spin.htm > > > I was trying to look at the above example page but when I click on the > links nothing happens. Looking at my Javascript console I see: > > Error: applet.getPropertyAsJSON is not a function > Source File: > http://www.stolaf.edu/people/hansonr/jmol/test/json/Jmol-new.js > Line: 923 > > and > > Error: applet.script is not a function > Source File: > http://www.stolaf.edu/people/hansonr/jmol/test/json/Jmol-new.js > Line: 264 > > I'm running Firefox 1.0.4, JDK 1.5, Fedora Core 4. > > Is there something I need to install/setup? - I haven't kept up with the > browser/jdk requirements for the applet :( > > ------------------------------------------------------------------- > Rajarshi Guha <rx...@ps...> <http://jijo.cjb.net> > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > ------------------------------------------------------------------- > All seems condemned in the long run to approximate a state akin to > Gaussian noise. > -- James Martin > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting language > that extends applications into web and mobile media. Attend the live webcast > and join the prime developer group breaking into this new coding territory! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein |