On Mon, Dec 5, 2011 at 12:56 PM, Eric Martz <[email protected]>wrote:
> Dear Bob,
>
> 1. Yes indeed, I am able to save and restore coordinates (and I did
> not know I could do that!). However, what I wanted is to animate the
> restore, not to have it snap to the final position all at once. Is
> there some way to do that?
>
> OK, here is a (crude?) idea. I am aligning a Salmonella protein with
> an Aquifex protein. I could load the Salmonella protein twice (so I
> have 3 models in Jmol). Then compare ROTATE TRANSLATE Salmonella to
> Aquifex. Then to UNDO/REVERSE animate: compare ROTATE TRANSLATE the
> relocated Salmonella with the extra copy of the same (not visible)
> Salmonella molecule that has not been moved. (I have not tried this yet.)
>
> 2. save COORD and restore COORD are not yet in the docs.
>
>
Check that example -- you use
oldCoord = {1.1}.xyz.all
and then later, you do a compare TO those oldCoord. In the demo you see it
move slowly and seamlessly to the old coordinates. All done with the
compare command.
> 3. At examples-11, item 115, clicking the initial command gives
>
> JmolConstants.java ERROR: predefined set compile error:@tu nucleic &
> within(group,_a=48)
> compile error:end of expression expected
ooh, that's not good. Bad Jmol version
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=115
should fix that. Definitely follow that model there.
> Thanks, Eric
>
> At 12/4/11, Robert Hanson wrote:
> >oops!
> ><http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=115>
> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=115
> >
> >You have to save the initial coordinates, that's all.
> >
> >
> >On Sun, Dec 4, 2011 at 5:11 PM, Eric Martz
> ><<mailto:[email protected]>[email protected]> wrote:
> >I have two protein molecules loaded as two separate models. The
> >following compare command works wonderfully, producing an entrancing
> >alignment animation:
> >
> >
> >compare {1.1} {2.1} SUBSET {*.ca} ATOMS {71-165} {94-188} {166-357}
> >{624-815} ROTATE TRANSLATE
> >
> >
> >Question:
> >
> >What is the easiest way to produce the reverse animation, making the
> >aligned chain move smoothly away from the target chain, back to its
> >position before the compare command?
> >
> >Thanks, -Eric
> >
> >
>
> >------------------------------------------------------------------------------
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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>
> http://www.stolaf.edu/people/hansonr
> >phone: <tel:507-786-3107>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>
> 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
>
> >------------------------------------------------------------------------------
> >All the data continuously generated in your IT infrastructure
> >contains a definitive record of customers, application performance,
> >security threats, fraudulent activity, and more. Splunk takes this
> >data and makes sense of it. IT sense. And common sense.
> >http://p.sf.net/sfu/splunk-novd2d
> >_______________________________________________
> >Jmol-users mailing list
> >[email protected]
> >https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> 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
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
_______________________________________________
Jmol-users mailing list
[email protected]
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