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 <djohnsto...@gmail.com> 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 <hans...@stolaf.edu> wrote:
>
>> Dean, I just checked in code that does this better.
>>
>> Bob
>>
>>
>> On Mon, Mar 1, 2010 at 10:38 PM, Robert Hanson <hans...@stolaf.edu>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
>>> <djohnsto...@gmail.com>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. 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
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