I can't reproduce your problem. for me,

rotate quaternion @q  

where q is a quaternion works fine. That Java method seems to be working correctly --

write coord t.mol

uses that, and it works for me. So it must be something in your code.

On Thu, Feb 27, 2014 at 12:37 PM, jiayi.zhou <jiayi.zhou@mun.ca> wrote:
Hi, I was trying to use Jmol's functions to build an app for my own need. I met a strange problem when I was using the function transformP2.
For example, I use Measure.getQuaternion() to get a quaternion. Let's call it q. Then I use q.transformP2(ptA,ptAnew) to get every atom's coordinates of a structure after rotation.

Then I also used Jmol script "rotate QUATERNION {q.q1 q.q2 q.q3 q.q0} to rotate the structure and then get the coordinates.

I notice the coordinates I get from these two ways are not equal. I found out that the coordinates I got by function transformP2 are correct. The coordinates I got by using rotate script are not. Do you know why? 

Thank you
Aiden/Jiayi Zhou

Office Tel: 709-864-4891
Master Candidate                    
Dept. of Computer Science             
Memorial University of Newfoundland  
St. John's, NL, Canada, A1B 3X5 
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