[MMTK] Vector Madness

Konrad Hinsen hinsen at cnrs-orleans.fr
Tue Sep 19 18:22:45 CEST 2006

On Sep 19, 2006, at 15:39, Dr. Seth Olsen wrote:

> Traceback (most recent call last):
>   File "<stdin>", line 37, in ?
>   File "/usr/lib/python2.4/site-packages/MMTK/Collections.py", line  
> 246, in normalizePosition
>     self.translateTo(Vector(0., 0., 0.))
>   File "/usr/lib/python2.4/site-packages/MMTK/Collections.py", line  
> 243, in translateTo
>     self.translateBy(position-self.centerOfMass())
>   File "/usr/lib/python2.4/site-packages/MMTK/Collections.py", line  
> 86, in centerOfMass
>     mr = mr + a._mass * a.position(conf)
>   File "Scientific_vector.pyx", line 74, in  
> Scientific_vector.vector.__add__
> TypeError: Argument 'other' has incorrect type (expected  
> Scientific_vector.vector, got array)

Which version of ScientificPython are you using? This works fine for  
me using the latest one (2.5.11).

On Sep 19, 2006, at 17:57, Dr. Seth Olsen wrote:

> Upon looking into the archives, I think I found the solution: to  
> delete the Scientific_vector.so file so that the original python  
> code is used.  If I'm wrong, I'll find out soon enough.

If you have an old Scientific with a buggy Pyrex vector class, that's  
a solution indeed.

> By the way, was the issue with the not-so-good fit via  
> findTransformation() ever solved?  That function works now for me  
> (as does most everything - thanks to everyone's help) but I must  
> admit that I've seen better rms fits from fortran qtrfit codes...

The function is supposed to produce the best fit possible using  
translation and rotation. If you have a case for which some other  
code produces a better fit, I'd like to see it to check what's going  

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr

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