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 <hans...@stolaf.edu> 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 <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
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>>>>> _______________________________________________
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>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> 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
> _______________________________________________
> 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
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