Bob,
Three points:
1) It works like a charm, at least with 2-butanol. I understand what
each line in your script is "saying," but I never could have come up
with this on my own!
2) The find axis component of the script will be of general use to me.
I've been agonizing over drawing initial structures to align with the
molecular xyz axis to pre wire structures for Jmol animation scripts.
It seems that there is no need for this. I need to take a closer look
at the Jmol math features. I'm embarrassed to admit that I did not
know that the vector math in your script was a Jmol option.
3) I've casually followed the user group for many years, but I only
recently started asking group questions related to the rebirth of an
old Jmol project. I don't know the protocol for requests or key words,
can you point me?
Otis
On Tue, Feb 2, 2010 at 12:38 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> Otis,
>
> It would be good to implement that. Feature request! Suggest a keyword
> option that would describe this.
>
> There is a scripting way to do this. You find the axis perpendicular to the
> two groups, determine the angle required, and rotate one CW while the other
> CCW.
>
> Given center {C} and two attached carbons, {Ca} and {Cb}, then:
>
> v1 = {Ca}.xyz - {C}.xyz
> v2 = {Cb}.xyz - {C}.xyz
> theAxis = cross(v1, v2)
> theAngle = angle(v1, {0 0 0}, v2)
>
> the two groups are found using select within(BRANCH,....)
> Then you do rotateSelected:
>
> select within(BRANCH, {C}, {Ca})
> rotateSelected MOLECULAR {C} @theAxis @theAngle
> select within(BRANCH, {C}, {Cb})
> rotateSelected MOLECULAR {C} @theAxis @{-theAngle}
>
> Should do the trick.
>
>
> Bob
> On Tue, Feb 2, 2010 at 10:36 AM, Otis Rothenberger <o...@chemagic.com>
> wrote:
>>
>> Hello-
>>
>> I'm trying to invert the configuration of a single carbon atom. The
>> symmetry operation of invertSelected inverts the configuration of
>> target atom attached carbon atoms as well as the target. I tried
>> selecting only the four target atom attached carbon atoms and then
>> cleaning up with a minimize. Interesting visual, but again neighboring
>> atom configuration is inverted after minimization.
>>
>> Three questions:
>>
>> 1) Am I missing another invertSelected possibility?
>> 2) Alternatively, is there a general scripting approach to simply swap
>> two groups attached to the target atom?
>> 3) Is there an alternative scripting path to my objective?
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> http://chemagic.org
>>
>>
>> ------------------------------------------------------------------------------
>> The Planet: dedicated and managed hosting, cloud storage, colocation
>> Stay online with enterprise data centers and the best network in the
>> business
>> Choose flexible plans and management services without long-term contracts
>> Personal 24x7 support from experience hosting pros just a phone call away.
>> http://p.sf.net/sfu/theplanet-com
>> _______________________________________________
>> 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
>
> ------------------------------------------------------------------------------
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the
> business
> Choose flexible plans and management services without long-term contracts
> Personal 24x7 support from experience hosting pros just a phone call away.
> http://p.sf.net/sfu/theplanet-com
>
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Otis Rothenberger
http://chemagic.org
------------------------------------------------------------------------------
The Planet: dedicated and managed hosting, cloud storage, colocation
Stay online with enterprise data centers and the best network in the business
Choose flexible plans and management services without long-term contracts
Personal 24x7 support from experience hosting pros just a phone call away.
http://p.sf.net/sfu/theplanet-com
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
