On 10/7/2010 9:11 AM, Robert Hanson wrote:
Well, it's symmetry axis is along Z, so just shorten or lengthen Z to change the opening angle. Or change X and Y distances. Right?
Yes, it works. Changing the z value (I presume) in vector type "2" changes the opening angle by moving the apex of the cone away from the origin along the z axis. So if I want to bring the apex back to the origin, I need to adjust the "z value" (I presume) of the origin from -5.0 to ?. My question is what is the relationship between these numbers.
Thanks for your help and your patience. PMPS. [I do not (obviously) understand how the cone was constructed and what are the meanings of the volume vectors and how is the origin defined, so it is all by trial and error].
On Wed, Oct 6, 2010 at 12:30 PM, Pshemak Maslak <p...@chem.psu.edu <mailto:p...@chem.psu.edu>> wrote:On 10/4/2010 1:14 PM, Robert Hanson wrote:yes, I think so. Just adjust the vector parameters to make it any size you want.The top of the jvxl file with the cone: [...] functionXY curveAsStringXY -2 -5.0 -5.0 -5.0 ANGSTROMS </jvxlFileTitle> <jvxlVolumeData origin="{-5.0 -5.0 -5.0}"> <<<< changing these changes origin <jvxlVolumeVector type="0" count="51" vector="{0.2 0.0 0.0}"></jvxlVolumeVector> <<<< changing these changes size <jvxlVolumeVector type="1" count="51" vector="{0.0 0.2 0.0}"></jvxlVolumeVector> <<<< changing these changes size <jvxlVolumeVector type="2" count="51" vector="{0.0 0.0 0.2}"></jvxlVolumeVector> <<<< changing these changes size [....] I can change the origin, or size or make it elliptic (if the vectors are not the same), but I do not know how to change the opening angle. Thanks for your help, PMOn Mon, Oct 4, 2010 at 11:08 AM, Pshemak Maslak <p...@chem.psu.edu <mailto:p...@chem.psu.edu>> wrote: On 10/1/2010 11:04 PM, Robert Hanson wrote: > > I lied. OK, see the JVXL file at > > http://stolaf.edu/people/hansonr/chemapps/jmol/docs/misc/cone.jvxl > > for a the surface z = sqrt(x^2 + y^2). Because it is a JVXL file, you > can go in and change the axes, change the scaling, change the origin, > etc., and have any cone you want. Even elliptical cones. Thank you very much for creating this nice cone. Can I change its opening angle directly in the jvxl file? > > This was created at > > http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm?USSIGNEDAPPLET&topic=14 <http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm?USSIGNEDAPPLET&topic=14> > <http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm?USSIGNEDAPPLET&topic=14 <http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm?USSIGNEDAPPLET&topic=14>> > > by entering > > Math.sqrt(x^2 + y^2) into the input box, clicking the link discussed > there to "set the function" and then issuing the following on the > command line: > > javascript "x0=-5;y0=-5;dx=.2;dy=.2";isosurface functionXY > "curveAsStringXY" {-5 -5 -5} {-51 0.2 0 0} {51 0 0.2 0} {51 0 0 0.2}; > > followed by > > write isosurface "cone.jvxl" I tried that (under item 14, after zapping the preloaded model). I entered "Math.sqrt(x^2 + y^2)" into the box and clicked the "click here to set the function" link (confirmed by the message window). After entering the script (above) on the command line I am getting a very complicated "egg-box" shape. If I do not click on the "click here to set the function" link I get a half of an ellipsoid (a "cone" with parabolic cross-sections) with the above script.. I am sure I am doing something wrong. All below is above my head (I speak no programming language :-(). And that is my problem. Thanks for your help, PM > > > That instructs Jmol to get the Z coordinate of the function from the > JavaScript function curveAsStringXY, which reads: > > function curveAsStringXY(app, nX, nY) { > var i1 = Math.abs(parseInt(""+nX)); > var i2 = Math.abs(0.0 + parseInt(""+nY)); > var s = "" > for (var i = 0; i < i1; i++) > for (var j = 0; j < i2; j++) { > s+= curveXY("",i, j) + "\n"; > } > return s; > > } > > > x0 = 0 > y0 = 0 > dx = 1 > dy = 1 > x = 0 > y = 0 > > function curveXY(app, ix, iy) { > setXY(ix, iy) > return eval(myfunction); > } > > function setXY(ix, iy) { > x = ix * dx + x0 > y = iy * dy + y0 > } > > > function setFunction(f,isSilent){ > myfunction = > (arguments.length<1?document.getElementById("fOfXY").value:f) > var x=1 > var y=1 > var z=NaN > try{eval("z="+myfunction)}catch(e){alert(e)} > if(isNaN(z)){ > alert("Your function is invalid") > myfunction = "(x*x+y*y)" > } > try{curveXY("",1,1)}catch(e){alert(e);return} > if (!isSilent)alert("The function Jmol will use is now z=" + > myfunction) > } > > myfunction = "(x*x + y*y)/3" > setFunction(myfunction,1) > > ------------------------------------------------------------------------------ Virtualization is moving to the mainstream and overtaking non-virtualized environment for deploying applications. Does it make network security easier or more difficult to achieve? Read this whitepaper to separate the two and get a better understanding. http://p.sf.net/sfu/hp-phase2-d2d _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/jmol-users-- Robert M. HansonProfessor 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 ------------------------------------------------------------------------------ Virtualization is moving to the mainstream and overtaking non-virtualized environment for deploying applications. Does it make network security easier or more difficult to achieve? Read this whitepaper to separate the two and get a better understanding. http://p.sf.net/sfu/hp-phase2-d2d _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/jmol-users------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net <mailto:Jmol-users@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb
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