[Jmol-users] Multiple clipping planes (using slab/depth HKL)
Jmol Users, Here's something I've always wanted to do with Jmol -- use clipping planes to show students the *fractions* of atoms in a unit cell (similar to attached image of NaCl generated using POV-Ray). I know I can use slab HKL and depth HKL, but those don't "slice" through the atoms like the normal slab and depth commands. I think there was a thread a while back on something like this, but I couldn't track it down. I've also thought about generating isosurfaces to represent the fractions of atoms, but that seemed tedious. Dean <>-- 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Multiple clipping planes (using slab/depth HKL)
You're on your own, I'm afraid. The atom "balls" are really 2D illusions created in the graphics engiine. They don't have any 3D counterpart whatsoever. On Fri, Feb 26, 2010 at 10:48 PM, Dean Johnston wrote: > Jmol Users, > > Here's something I've always wanted to do with Jmol -- use clipping > planes to show students the *fractions* of atoms in a unit cell (similar > to attached image of NaCl generated using POV-Ray). I know I can use slab > HKL and depth HKL, but those don't "slice" through the atoms like the normal > slab and depth commands. I think there was a thread a while back on > something like this, but I couldn't track it down. I've also thought about > generating isosurfaces to represent the fractions of atoms, but that seemed > tedious. > > Dean > > > -- > 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 > 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 -- 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Multiple clipping planes (using slab/depth HKL)
Well, that wasn't so bad.
isosurface na1 cap unitcell center {atomno=1} sphere 2.0
does what you see there for one of the atoms
isosurface na1 slab unitcell center {atomno=1} sphere 2.0
does that, but doesn't close the ends. Kind of cool that this addition only
about 20 lines of code. Fun!
So the solution is to create a sphere isosurface for each.
Kind of neat that the unitcell doesn't have to be orthogonal.
Also works with boundbox.
Bob
On Fri, Feb 26, 2010 at 10:48 PM, Dean Johnston wrote:
> Jmol Users,
>
> Here's something I've always wanted to do with Jmol -- use clipping
> planes to show students the *fractions* of atoms in a unit cell (similar
> to attached image of NaCl generated using POV-Ray). I know I can use slab
> HKL and depth HKL, but those don't "slice" through the atoms like the normal
> slab and depth commands. I think there was a thread a while back on
> something like this, but I couldn't track it down. I've also thought about
> generating isosurfaces to represent the fractions of atoms, but that seemed
> tedious.
>
> Dean
>
>
> --
> 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
> 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
--
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
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Multiple clipping planes (using slab/depth HKL)
Dean, I just checked in code that does this better.
Bob
On Mon, Mar 1, 2010 at 10:38 PM, Robert Hanson wrote:
> Well, that wasn't so bad.
>
> isosurface na1 cap unitcell center {atomno=1} sphere 2.0
>
> does what you see there for one of the atoms
>
> isosurface na1 slab unitcell center {atomno=1} sphere 2.0
>
> does that, but doesn't close the ends. Kind of cool that this addition only
> about 20 lines of code. Fun!
>
> So the solution is to create a sphere isosurface for each.
>
> Kind of neat that the unitcell doesn't have to be orthogonal.
>
> Also works with boundbox.
>
> Bob
>
> On Fri, Feb 26, 2010 at 10:48 PM, Dean Johnston wrote:
>
>> Jmol Users,
>>
>> Here's something I've always wanted to do with Jmol -- use clipping
>> planes to show students the *fractions* of atoms in a unit cell (similar
>> to attached image of NaCl generated using POV-Ray). I know I can use slab
>> HKL and depth HKL, but those don't "slice" through the atoms like the normal
>> slab and depth commands. I think there was a thread a while back on
>> something like this, but I couldn't track it down. I've also thought about
>> generating isosurfaces to represent the fractions of atoms, but that seemed
>> tedious.
>>
>> Dean
>>
>>
>> --
>> 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
>> 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
--
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
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Multiple clipping planes (using slab/depth HKL)
Oh - this is great! Exactly what I wanted - in a straightforward
implementation - nicely done. Thanks Bob!
Dean
On Tue, Mar 2, 2010 at 8:20 AM, Robert Hanson wrote:
> Dean, I just checked in code that does this better.
>
> Bob
>
>
> On Mon, Mar 1, 2010 at 10:38 PM, Robert Hanson wrote:
>
>> Well, that wasn't so bad.
>>
>> isosurface na1 cap unitcell center {atomno=1} sphere 2.0
>>
>> does what you see there for one of the atoms
>>
>> isosurface na1 slab unitcell center {atomno=1} sphere 2.0
>>
>> does that, but doesn't close the ends. Kind of cool that this addition
>> only about 20 lines of code. Fun!
>>
>> So the solution is to create a sphere isosurface for each.
>>
>> Kind of neat that the unitcell doesn't have to be orthogonal.
>>
>> Also works with boundbox.
>>
>> Bob
>>
>> On Fri, Feb 26, 2010 at 10:48 PM, Dean Johnston wrote:
>>
>>> Jmol Users,
>>>
>>> Here's something I've always wanted to do with Jmol -- use clipping
>>> planes to show students the *fractions* of atoms in a unit cell (similar
>>> to attached image of NaCl generated using POV-Ray). I know I can use slab
>>> HKL and depth HKL, but those don't "slice" through the atoms like the normal
>>> slab and depth commands. I think there was a thread a while back on
>>> something like this, but I couldn't track it down. I've also thought about
>>> generating isosurfaces to represent the fractions of atoms, but that seemed
>>> tedious.
>>>
>>> Dean
>>>
>>>
>>> --
>>> 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
>>> 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
>
>
> --
> 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
> Jmol-users@lists.sourceforge.net
> 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
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Multiple clipping planes (using slab/depth HKL)
Better than that.
Dean, once again you have such a great idea, and I am delighted to say it
was relatively easy to implement. Here's what I just checked in:
LcaoCartoon now has a "CPK" option. This option creates a sphere at the
radius of the currently set spacefill. (The "s" option creates a sphere of a
standard radius.) That may seem a bit odd, but the idea is that you can set
the radius using spacefill and then apply that radius to LCAOCARTOON for
this special purpose.
Why LcaoCartoon? Because LcaoCartoon is a form of isosurface, and it allows
tying an isosurface to a specific atom.
And since isosurfaces now can be slabbed and capped by planes,
boundingboxes, and unitcells, so can LcaoCartoons.
So here's how you would do that:
select {theAtoms}
spaceFill 2.0 # perhaps
color translucent blue # color also used in lcaocartoon CPK method
lcaocartoon CAP unitcell cpk
spaceFill off
If this seems too weird, we can talk about another way of doing it, but for
now this should work.
Bob
On Wed, Mar 3, 2010 at 7:44 AM, Dean Johnston wrote:
> Oh - this is great! Exactly what I wanted - in a straightforward
> implementation - nicely done. Thanks Bob!
>
> Dean
>
>
> On Tue, Mar 2, 2010 at 8:20 AM, Robert Hanson wrote:
>
>> Dean, I just checked in code that does this better.
>>
>> Bob
>>
>>
>> On Mon, Mar 1, 2010 at 10:38 PM, Robert Hanson wrote:
>>
>>> Well, that wasn't so bad.
>>>
>>> isosurface na1 cap unitcell center {atomno=1} sphere 2.0
>>>
>>> does what you see there for one of the atoms
>>>
>>> isosurface na1 slab unitcell center {atomno=1} sphere 2.0
>>>
>>> does that, but doesn't close the ends. Kind of cool that this addition
>>> only about 20 lines of code. Fun!
>>>
>>> So the solution is to create a sphere isosurface for each.
>>>
>>> Kind of neat that the unitcell doesn't have to be orthogonal.
>>>
>>> Also works with boundbox.
>>>
>>> Bob
>>>
>>> On Fri, Feb 26, 2010 at 10:48 PM, Dean Johnston
>>> wrote:
>>>
Jmol Users,
Here's something I've always wanted to do with Jmol -- use clipping
planes to show students the *fractions* of atoms in a unit cell
(similar to attached image of NaCl generated using POV-Ray). I know I can
use slab HKL and depth HKL, but those don't "slice" through the atoms like
the normal slab and depth commands. I think there was a thread a while
back
on something like this, but I couldn't track it down. I've also thought
about generating isosurfaces to represent the fractions of atoms, but that
seemed tedious.
Dean
--
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
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
>>
>>
>> --
>> 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
>> Jmol-users@lists.sourceforge.net
>> 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
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Ola
Re: [Jmol-users] Multiple clipping planes (using slab/depth HKL)
Yes - you're ahead of me again. I like having the isosurfaces tied to atoms
- certainly easier than creating one for each atom. I can't wait to set up
some web pages using this...
Dean
On Wed, Mar 3, 2010 at 8:45 AM, Robert Hanson wrote:
> Better than that.
>
> Dean, once again you have such a great idea, and I am delighted to say it
> was relatively easy to implement. Here's what I just checked in:
>
> LcaoCartoon now has a "CPK" option. This option creates a sphere at the
> radius of the currently set spacefill. (The "s" option creates a sphere of a
> standard radius.) That may seem a bit odd, but the idea is that you can set
> the radius using spacefill and then apply that radius to LCAOCARTOON for
> this special purpose.
>
> Why LcaoCartoon? Because LcaoCartoon is a form of isosurface, and it allows
> tying an isosurface to a specific atom.
> And since isosurfaces now can be slabbed and capped by planes,
> boundingboxes, and unitcells, so can LcaoCartoons.
>
> So here's how you would do that:
>
> select {theAtoms}
> spaceFill 2.0 # perhaps
> color translucent blue # color also used in lcaocartoon CPK method
> lcaocartoon CAP unitcell cpk
> spaceFill off
>
> If this seems too weird, we can talk about another way of doing it, but for
> now this should work.
>
> Bob
>
>
>
>
> On Wed, Mar 3, 2010 at 7:44 AM, Dean Johnston wrote:
>
>> Oh - this is great! Exactly what I wanted - in a straightforward
>> implementation - nicely done. Thanks Bob!
>>
>> Dean
>>
>>
>> On Tue, Mar 2, 2010 at 8:20 AM, Robert Hanson wrote:
>>
>>> Dean, I just checked in code that does this better.
>>>
>>> Bob
>>>
>>>
>>> On Mon, Mar 1, 2010 at 10:38 PM, Robert Hanson wrote:
>>>
Well, that wasn't so bad.
isosurface na1 cap unitcell center {atomno=1} sphere 2.0
does what you see there for one of the atoms
isosurface na1 slab unitcell center {atomno=1} sphere 2.0
does that, but doesn't close the ends. Kind of cool that this addition
only about 20 lines of code. Fun!
So the solution is to create a sphere isosurface for each.
Kind of neat that the unitcell doesn't have to be orthogonal.
Also works with boundbox.
Bob
On Fri, Feb 26, 2010 at 10:48 PM, Dean Johnston
wrote:
> Jmol Users,
>
> Here's something I've always wanted to do with Jmol -- use clipping
> planes to show students the *fractions* of atoms in a unit cell
> (similar to attached image of NaCl generated using POV-Ray). I know I can
> use slab HKL and depth HKL, but those don't "slice" through the atoms like
> the normal slab and depth commands. I think there was a thread a while
> back
> on something like this, but I couldn't track it down. I've also thought
> about generating isosurfaces to represent the fractions of atoms, but that
> seemed tedious.
>
> Dean
>
>
> --
> 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
> 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
>>>
>>>
>>> --
>>> 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
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> --
>> Download Intel® Parallel Studio Eval
>> Try the new software tools for yourself.
