Dan, please try this:
http://chemapps.stolaf.edu/jmol/Jmol-13.zip
and let me know if that is better.
Thanks for spotting this,
Bob
On Thu, Feb 28, 2013 at 10:18 PM, Robert Hanson <[email protected]> wrote:
> well, we'll have to fix that. Here's the calc:
>
> public static float getRmsd(P3[][] centerAndPoints, Quaternion q) {
> double sum = 0;
> double sum2 = 0;
> int n = centerAndPoints[0].length - 1;
> P3 ptAnew = new P3();
> for (int i = n + 1; --i >= 1;) {
> ptAnew.setT(centerAndPoints[0][i]);
> ptAnew.sub(centerAndPoints[0][0]);
> q.transformP2(ptAnew, ptAnew);
> ptAnew.add(centerAndPoints[1][0]);
> double d = ptAnew.distance(centerAndPoints[1][i]);
> sum += d;
> sum2 += d * d;
> }
> return (float) Math.sqrt((sum2 - sum * sum / n) / (n - 1));
> }
>
> OK, my bad. That's a sample distribution. Bet it should be the following,
> right?
>
>
> public static float getRmsd(P3[][] centerAndPoints, Quaternion q) {
> double sum2 = 0;
> int n = centerAndPoints[0].length - 1;
> P3 ptAnew = new P3();
> for (int i = n + 1; --i >= 1;) {
> ptAnew.setT(centerAndPoints[0][i]);
> ptAnew.sub(centerAndPoints[0][0]);
> q.transformP2(ptAnew, ptAnew);
> ptAnew.add(centerAndPoints[1][0]);
> sum2 += ptAnew.distanceSquared(centerAndPoints[1][i]);
> }
> return (float) Math.sqrt(sum2 / n);
> }
>
>
>
>
>
> On Thu, Feb 28, 2013 at 6:35 PM, Dan Kirshner <[email protected]>wrote:
>
>> The compare command appears to align atoms correctly -- that is, it
>> appears to give the same results as Chimera.
>>
>> The RMSD it reports in the Java console, however, does not match my
>> calculations (which do match Chimera!). I haven't been able to figure out
>> what Jmol _is_ reporting, but I'm hoping someone (OK, Bob) can add this to
>> his to-do list.
>>
>> Thanks!
>>
>> --Dan
>>
>>
>> ------------------------------------------------------------------------------
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>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
------------------------------------------------------------------------------
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