From: Robert H. <ha...@st...> - 2010-03-28 02:46:48
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Jmol users, http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm OK, we are going to have fun with this! Jmol now has atom-pair comparisons built into the scripting in the form of a COMPARE command and also a nifty ROTATE option: ROTATE COMPARE {atoms1} {atoms2} -nSeconds does a smooth motion animation over nSeconds time moving atoms1 to the absolute best fit at the positions of atoms2 in a straight line motion. It's really a combination of a rotation and a translation -- which, by the way, constitutes a helical or screw motion. (The negative sign is necessary because for the rotate command, a positive number is degrees per second.) So there is also a HELIX option that lets you visualize that screw motion. (I'm betting Dean Johnston is getting ideas already....) ROTATE HELIX COMPARE {atoms1} {atoms2} -nSeconds Note that you need at least 3 atoms to do this. Otherwise the pathway is undefined. Watch those crystallographic molecules zoom around their screw axes: ROTATE HELIX COMPARE {symop=1} {symop=4} -3 right? (no, we can't invert through a plane or center of inversion yet...) Also, you can compare two sets, but then move another based on that comparison: ROTATE COMPARE {2.1 and *.CA} {1.1 and *.CA} {2.1} -3 This moves the whole model 2.1 based on a comparison of just the alpha carbons -- what PyMol and other programs typically do, without the fun of animation. Also, in this release will be the organic chemist's stereochemical inversion, which is technically a 180-degree rotation. A nice example of that is up there as well as feature #110. It looks like this: select {*} invertSelected STEREO {atomno=12} {atomno=11 or atomno=13} This will invert the groups around atomno=12 that are NOT atoms 11 or 13. Hmm. Come to think of it, I should probably change that to the center and the atoms you DO want inverted, right? OK.... This one's not quite ready, I think. Bob -- 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: Paul P. <pau...@ac...> - 2010-03-28 12:11:13
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Congratulations Bob, this is really awesome ! I was wondering if it would be possible to make such a structural alignment between two different applets included in the same webpage ? Once both molecules are aligned, the applets could be synchronized thus allowing a comparison between both structures. Thanks, Paul Le 28 mars 2010 à 04:46, Robert Hanson a écrit : > Jmol users, > > > http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm > > OK, we are going to have fun with this! Jmol now has atom-pair comparisons built into the scripting in the form of a COMPARE command and also a nifty ROTATE option: > > > ROTATE COMPARE {atoms1} {atoms2} -nSeconds > > does a smooth motion animation over nSeconds time moving atoms1 to the absolute best fit at the positions of atoms2 in a straight line motion. It's really a combination of a rotation and a translation -- which, by the way, constitutes a helical or screw motion. (The negative sign is necessary because for the rotate command, a positive number is degrees per second.) So there is also a HELIX option that lets you visualize that screw motion. (I'm betting Dean Johnston is getting ideas already....) > > ROTATE HELIX COMPARE {atoms1} {atoms2} -nSeconds > > Note that you need at least 3 atoms to do this. Otherwise the pathway is undefined. Watch those crystallographic molecules zoom around their screw axes: > > ROTATE HELIX COMPARE {symop=1} {symop=4} -3 > > right? (no, we can't invert through a plane or center of inversion yet...) > > Also, you can compare two sets, but then move another based on that comparison: > > ROTATE COMPARE {2.1 and *.CA} {1.1 and *.CA} {2.1} -3 > > This moves the whole model 2.1 based on a comparison of just the alpha carbons -- what PyMol and other programs typically do, without the fun of animation. > > Also, in this release will be the organic chemist's stereochemical inversion, which is technically a 180-degree rotation. A nice example of that is up there as well as feature #110. It looks like this: > > select {*} > invertSelected STEREO {atomno=12} {atomno=11 or atomno=13} > > This will invert the groups around atomno=12 that are NOT atoms 11 or 13. Hmm. Come to think of it, I should probably change that to the center and the atoms you DO want inverted, right? OK.... This one's not quite ready, I think. > > > Bob > > > -- > 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 > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Robert H. <ha...@st...> - 2010-03-28 13:16:29
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Absolutely! Or just have one applet send the information to the other. All it is is a quaternion (4 numbers) and a translation vector (3 numbers). You could write that today in about 5 minutes, I think. Pretty easy, because with SYNC you have direct applet-applet communication without JavaScript. Bob On Sun, Mar 28, 2010 at 7:11 AM, Paul Pillot < pau...@ac...> wrote: > Congratulations Bob, this is really awesome ! > I was wondering if it would be possible to make such a structural alignment > between two different applets included in the same webpage ? > Once both molecules are aligned, the applets could be synchronized thus > allowing a comparison between both structures. > Thanks, > Paul > Le 28 mars 2010 à 04:46, Robert Hanson a écrit : > > Jmol users, > > > http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm > > OK, we are going to have fun with this! Jmol now has atom-pair comparisons > built into the scripting in the form of a COMPARE command and also a nifty > ROTATE option: > > > ROTATE COMPARE {atoms1} {atoms2} -nSeconds > > does a smooth motion animation over nSeconds time moving atoms1 to the > absolute best fit at the positions of atoms2 in a straight line motion. It's > really a combination of a rotation and a translation -- which, by the way, > constitutes a helical or screw motion. (The negative sign is necessary > because for the rotate command, a positive number is degrees per second.) So > there is also a HELIX option that lets you visualize that screw motion. (I'm > betting Dean Johnston is getting ideas already....) > > ROTATE HELIX COMPARE {atoms1} {atoms2} -nSeconds > > Note that you need at least 3 atoms to do this. Otherwise the pathway is > undefined. Watch those crystallographic molecules zoom around their screw > axes: > > ROTATE HELIX COMPARE {symop=1} {symop=4} -3 > > right? (no, we can't invert through a plane or center of inversion yet...) > > Also, you can compare two sets, but then move another based on that > comparison: > > ROTATE COMPARE {2.1 and *.CA} {1.1 and *.CA} {2.1} -3 > > This moves the whole model 2.1 based on a comparison of just the alpha > carbons -- what PyMol and other programs typically do, without the fun of > animation. > > Also, in this release will be the organic chemist's stereochemical > inversion, which is technically a 180-degree rotation. A nice example of > that is up there as well as feature #110. It looks like this: > > select {*} > invertSelected STEREO {atomno=12} {atomno=11 or atomno=13} > > This will invert the groups around atomno=12 that are NOT atoms 11 or 13. > Hmm. Come to think of it, I should probably change that to the center and > the atoms you DO want inverted, right? OK.... This one's not quite ready, I > think. > > > Bob > > > -- > 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 > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > 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 |