[Jmol-users] drawing cones
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.
This was created at
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"
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)
On Fri, Oct 1, 2010 at 9:26 PM, Robert Hanson wrote:
> Sorry, no good way to do that.
>
> On Fri, Oct 1, 2010 at 4:03 PM, Pshemak Maslak wrote:
>
>> How can I draw open right cones in Jmole?
>>
>> For example, how can draw the double cone for nodal surface of 3d(z^2)
>> orbital?
>>
>> Thanks, for your help.
>>
>> PM
>>
>>
>> --
>> Start uncovering the many advantages of virtual appliances
>> and start using them to simplify application deployment and
>> accelerate your shift to cloud computing.
>> http://p.sf.net/sfu/novell-sfdev2dev
>> ___
>> Jmol-users mailing list
>> 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
>
--
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
--
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
--
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] drawing cones
Sorry, no good way to do that. On Fri, Oct 1, 2010 at 4:03 PM, Pshemak Maslak wrote: > How can I draw open right cones in Jmole? > > For example, how can draw the double cone for nodal surface of 3d(z^2) > orbital? > > Thanks, for your help. > > PM > > > -- > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > ___ > Jmol-users mailing list > 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 -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] drawing cones
How can I draw open right cones in Jmole? For example, how can draw the double cone for nodal surface of 3d(z^2) orbital? Thanks, for your help. PM -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and DSSP
a big "YES" from here too! That would be great -Tom On Thu, Sep 30, 2010 at 8:30 PM, Robert Hanson wrote: > Jmol users interested in protein visualization: > > Is there any interest in having Jmol be able to calculate (verifiably > proper) DSSP secondary structure for proteins -- alpha helices, 3/10 > helices, pi-helices, turns, antiparallel and parallel ladders, etc.? > > Thanks. > > 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 > > > -- > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and DSSP
The coding is done. I'm using a totally different approach to the coding, not just a translation of Pascal to C to Java. MUCH simpler! Bob On Fri, Oct 1, 2010 at 2:11 AM, gilleain torrance < gilleain.torra...@gmail.com> wrote: > Hi, > > Yes, I would be very interested in this. However I warn you against > actually reading the dssp source as it was translated from fortran > with f2c and was pretty unreadable, as far as I remember :) > > gilleain > > On Fri, Oct 1, 2010 at 4:30 AM, Robert Hanson wrote: > > Jmol users interested in protein visualization: > > > > Is there any interest in having Jmol be able to calculate (verifiably > > proper) DSSP secondary structure for proteins -- alpha helices, 3/10 > > helices, pi-helices, turns, antiparallel and parallel ladders, etc.? > > > > Thanks. > > > > 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 > > > > > -- > > Start uncovering the many advantages of virtual appliances > > and start using them to simplify application deployment and > > accelerate your shift to cloud computing. > > http://p.sf.net/sfu/novell-sfdev2dev > > ___ > > Jmol-users mailing list > > Jmol-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > -- > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > ___ > Jmol-users mailing list > 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 -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] insert into database
Hello Aiswarya It can be done, but very much depends on how your database is organized and you query it. Please provide a sample page or page source code so we can give you some advice on specific terms. - The script for many molecules would be the same as for one. Or do you want to load several molecules together into the same Jmol? - "when clicked upon the molecule" What does this mean? Where would you click? -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] insert into database
hi, am creating a database so i would like to incorporate Jmol into the database but for that i have to write a script which would should show each molecule in Jmol when clicked upon the molecule. please if anyone has a script on how to load the particular molecule, i know the script for a single molecule but dont know for many molecules. Thanks. -- Aiswarya B Pawar aiswa...@vmsrf.org junior scientist Vittal mallya scientific research foundation banaglore -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and DSSP
Hi, Yes, I would be very interested in this. However I warn you against actually reading the dssp source as it was translated from fortran with f2c and was pretty unreadable, as far as I remember :) gilleain On Fri, Oct 1, 2010 at 4:30 AM, Robert Hanson wrote: > Jmol users interested in protein visualization: > > Is there any interest in having Jmol be able to calculate (verifiably > proper) DSSP secondary structure for proteins -- alpha helices, 3/10 > helices, pi-helices, turns, antiparallel and parallel ladders, etc.? > > Thanks. > > 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 > > -- > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
