From: Eric H. <eri...@un...> - 2012-04-23 04:09:03
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Thanks! Envoyé de mon iPhone Le 22 avr. 2012 à 21:43, Robert Hanson <ha...@st...> a écrit : > @pt1 @pt2 > > On Sun, Apr 22, 2012 at 1:48 PM, eric henon <eri...@un...> wrote: > Dear Robert, > > Once more, thanks for your help and advices. > > I'm going to draw my "own" box using the draw line instruction. > The points coordinates (updated by the user) will be stored in variables pt1 and pt2. > However I don't get to use the line command using variables. > > For ex. > > pt1=point(-2.,0.,0.); // (-2, 0, 0 will be stored in variables too.) > pt2=point(0.,2.,3.); > draw line pt1 pt2 > > doesn't work, > > nor > > draw line {pt1 pt2} > > nor > > draw line pt1.xyz pt2.xyz > > I tried a lot of syntaxes, unsuccessfully. > I did'nt find the response reading the Jmol documentation. > > Is it possible to use variables when using the line command ? > (Polygon prevents drawing quadrilateral, that's the reason why > I decided to use the line command instead). > Thanks in advance. > > Sincerely. > Eric > > > > > > Le 17 avr. 2012 à 04:04, Robert Hanson a écrit : > >> OK! Glad to hear that is working. The boundbox object is not any old box. It's always in the frame of xyz axes. You would have to design your own box based on something like a set of four DRAW polygons or something like that, and then change the points around that define its corners. Not super difficult, because you could take a set of points and rotate them with a matrix, but a fair challenge. Definitely could be done. Check out >> >> DRAW polygon >> >> http://chemapps.stolaf.edu/jmol/docs/#draw >> >> By the way, one would generally put all those scripts together with semicolons: >> >> jmolScript("boundbox {*};boundbox on;console;show boundbox;print getProperty('boundboxInfo','center');print getProperty('boundboxInfo','vector')"); >> >> for example. >> >> On Mon, Apr 16, 2012 at 6:42 PM, eric henon <eri...@un...> wrote: >> Dear all, >> >> thanks to Robert, >> I wrote the following code >> to be able to translate and rotate >> a bounding box (some line codes are still lacking, >> but all the data I need are below). >> >> Translating the box is easy. My problem, is that boundbox command >> always refer to the molecule axes through (center, vector) or >> (corner, corner), hence, using this command, it seems to me it is not possible >> to rotate the boundingbox independently >> of the molecule axes: the boundbox axes are always >> aligned on to the molecule axes. That's what I observe. >> >> Is there a way to rotate the bounding box independently >> of the molecule (thus around the molecule axes) ? >> >> Thanks in advance for your help. >> Sincerely. >> Eric >> >> ****** >> <html> >> <head> >> <title>Simple example</title> >> <script src="./Jmol.js" type="text/javascript"></script> >> </head> >> <body> >> <form> >> <script type="text/javascript"> >> jmolInitialize("."); // REQUIRED >> jmolSetAppletColor("skyblue"); // if you don't want black >> jmolApplet(800, "load 2PO6.pdb"); >> jmolBr(); >> // a radio group >> jmolHtml("atoms "); >> jmolRadioGroup([ >> ["spacefill off", "off"], >> ["spacefill 20%", "20%", "checked"], >> ["spacefill 100%", "100%"] >> ]); >> jmolBr(); >> // a button >> jmolButton("reset", "Reset to original orientation"); >> >> // axes >> jmolScript("axes MOLECULAR"); >> jmolScript("axes ON"); >> >> // a bound box >> jmolScript("boundbox {*}"); >> jmolScript("boundbox on"); >> jmolScript("console"); >> jmolScript("show boundbox"); >> >> jmolScript("print getProperty('boundboxInfo','center')"); >> jmolScript("print getProperty('boundboxInfo','vector')"); >> >> // jmolScript("bbic= getProperty('boundboxInfo','center')"); >> // jmolScript("print bbic.z"); >> >> // rotate boundbox >> // a link >> jmolBr(); >> jmolLink("boundbox CORNERS {25. 40. -15.} {15. 48. 31.}; show boundbox", "Rotate Box"); >> >> </script> >> </form> >> </body> >> </html> >> >> >> >> ****** >> >> >> Le 13 avr. 2012 à 13:18, eric henon a écrit : >> >>> Dear Robert, >>> >>> >>> Many thanks, indeed, for your detailed answer. >>> >>> That's exaclty the tools I was looking for. >>> Thus, I'am going to fully dedicate my attention to it now ! >>> >>> Thanks again. >>> Best regards. >>> Eric >>> >>> >>> Le 13 avr. 2012 à 06:48, Robert Hanson a écrit : >>> >>>> Oh, yes! Absolutely! You can place it anywhere you want, around any set of atoms, and then check its coordinates. >>>> >>>> For example: >>>> >>>> load =1crn >>>> boundbox {1-3} // first >>>> boundbox on >>>> show boundbox >>>> print boundboxinfo >>>> getProperty boundboxinfo >>>> print getProperty("BoundBoxInfo.corner1") >>>> x = getProperty("BoundBoxInfo.corner0") >>>> y = getProperty("BoundBoxInfo") >>>> print y["corner0"] >>>> >>>> That sort of thing. Also: >>>> >>>> boundbox scale 2.0 {1-3} >>>> >>>> boundbox {structureid="H2"} // second helix >>>> >>>> >>>> On Thu, Apr 12, 2012 at 7:41 PM, eric henon <eri...@un...> wrote: >>>> Hello, >>>> >>>> I'm new to Jmol; I'm interested >>>> in building, rotating, resizing >>>> an "independent" bounding box enclosing an active site >>>> in a protein, in order to finally get its cartesian coordinates. >>>> >>>> Is Jmol the appropriate tool/langage >>>> to do that ? >>>> >>>> Thanks in advance for your answer. >>>> Sincerely. >>>> Eric >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> For Developers, A Lot Can Happen In A Second. >>>> Boundary is the first to Know...and Tell You. >>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! >>>> http://p.sf.net/sfu/Boundary-d2dvs2 >>>> _______________________________________________ >>>> Jmol-developers mailing list >>>> Jmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>> >>>> >>>> >>>> -- >>>> 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 >>>> ------------------------------------------------------------------------------ >>>> For Developers, A Lot Can Happen In A Second. >>>> Boundary is the first to Know...and Tell You. >>>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! >>>> http://p.sf.net/sfu/Boundary-d2dvs2_______________________________________________ >>>> Jmol-developers mailing list >>>> Jmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>> >>> Eric Henon >>> Professeur >>> Universite de Reims Champagne-Ardenne >>> Institut de Chimie Moleculaire de Reims >>> http://www.univ-reims.fr/ICMR >>> CNRS UMR 6229 >>> UFR des Sciences Exactes et Naturelles >>> BP 1039 >>> 51687 Reims Cedex 2 (France) >>> Tél./Fax : + 33 (0) 3 26 91 84 97 >>> eri...@un... >>> >> >> >> Eric Henon >> Professeur >> Universite de Reims Champagne-Ardenne >> Institut de Chimie Moleculaire de Reims >> http://www.univ-reims.fr/ICMR >> CNRS UMR 6229 >> UFR des Sciences Exactes et Naturelles >> BP 1039 >> 51687 Reims Cedex 2 (France) >> Tél./Fax : + 33 (0) 3 26 91 84 97 >> eri...@un... >> >> >> ------------------------------------------------------------------------------ >> For Developers, A Lot Can Happen In A Second. >> Boundary is the first to Know...and Tell You. >> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! >> http://p.sf.net/sfu/Boundary-d2dvs2 >> >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> >> >> >> -- >> 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 >> ------------------------------------------------------------------------------ >> Better than sec? Nothing is better than sec when it comes to >> monitoring Big Data applications. Try Boundary one-second >> resolution app monitoring today. Free. >> http://p.sf.net/sfu/Boundary-dev2dev_______________________________________________ >> >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > Eric Henon > Professeur > Universite de Reims Champagne-Ardenne > Institut de Chimie Moleculaire de Reims > http://www.univ-reims.fr/ICMR > CNRS UMR 6229 > UFR des Sciences Exactes et Naturelles > BP 1039 > 51687 Reims Cedex 2 (France) > Tél./Fax : + 33 (0) 3 26 91 84 97 > eri...@un... > > > ------------------------------------------------------------------------------ > For Developers, A Lot Can Happen In A Second. > Boundary is the first to Know...and Tell You. > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! > http://p.sf.net/sfu/Boundary-d2dvs2 > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > > > -- > 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 > ------------------------------------------------------------------------------ > For Developers, A Lot Can Happen In A Second. > Boundary is the first to Know...and Tell You. > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! > http://p.sf.net/sfu/Boundary-d2dvs2 > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers |