Hi Johannes,
> I can use the function and commands. print clipped("clipsed") - but not
> print clipped("3lzt") - shows the indices of the atoms between the clipping
> planes
print clipped("3lzt") should print the indices of atoms that are
clipped off by the clipping planes. That works for me, but in terms of
the lines I sent, you may want to first save the clipping selection to
a variable.
> ATTENTION: The rotation matrix is in column-major order - that's
> understandable. Hence by multiplying with v[2], v[5] and v[8], you multiply
> the third column - not row! - with the coordinate vector, in order to get
> the rotated z-component. The matrix seems to be transposed. For me that is
> very unusual. In my R script, I made ordinary matrix multiplication and got
> erroneous results.
Well, the transpose is just the reverse rotation. It's merely a matter
of what the programmer had in mind when writing it :) In your R
script, you could just have tried t(R) %*% x in stead of R %*% x ;)
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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