OR:
load caffeine.xyz;
spin branch {N8} {C19} 50 # CH3 starts spinning around the N8-C19 bond
select connected(C19) and not N8
rotateSelected {N8} {C19} 30 # CH3 rotates 30 degrees around that bond
This second doesn't presume rotation about a bond. The two atoms, N8 and
C19, are simply defining an axis of rotation. That could be any two atoms or
any two points:
rotateSelected {0 0 0} {1 1 1} 30
or a defined axis and angle:
rotateSelected axisangle {1 1 1 30}
or, if an axis name is designated, make sure you use "molecular" to refer to
the molecular axis, not the window axes.
rotateSelected molecular x 30
Bob
On Mon, May 11, 2009 at 12:31 PM, Robert Hanson <[email protected]> wrote:
> You tried rotateSelected?
>
>
>
>
>
> On Mon, May 11, 2009 at 10:02 AM, Chris Foley <
> [email protected]> wrote:
>
>> Hi Jmol users,
>>
>> Is it is possible to translate atoms programmatically from within a Java
>> application? I have tried variations on the following but it does not
>> seem to work:
>>
>> Point3f p = viewer.getAtomPoint3f(jmolindex);
>> p.set(newXYZf);
>>
>> Tantalisingly, as the program executes I see the atoms move in Jmol and
>> then they snap back to their original positions. I have a working Jmol
>> script for this but because I want to translate a large number of atoms
>> different distances the script is proving too slow.
>>
>> To put this strange request in context, I am trying to rotate selected
>> atoms around a point, hence the need to "translate" the atoms
>> individually.
>>
>> Thanks in advance for any help.
>>
>> Cheers,
>> Chris.
>>
>>
>> ------------------------------------------------------------------------------
>> The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
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>> Kodak, there's a perfect scanner to get the job done! With the NEW KODAK
>> i700
>> Series Scanner you'll get full speed at 300 dpi even with all image
>> processing features enabled. http://p.sf.net/sfu/kodak-com
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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
------------------------------------------------------------------------------
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image
processing features enabled. http://p.sf.net/sfu/kodak-com
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