Orienting a Monoclinic Crystal

[gvandyke]

In the documentation for orienting monoclinic crystals in the lab frame, it says, "For short Hermann-Mauguin symbols (like P2, Cm, P21/m, etc), yC is along the unique axis...In all cases, the other two axes are arbitrary."

Why are the other two axes arbitrary if I need to align the xC, yC, and zC with xL, yL, and zL? Don't I need to know where the other two crystal axes are?

For example, I want to simulate a single spectrum where my crystal b-axis (yC) is along yL, and the crystal c-axis (13 degrees below zC/c*) is along zL. If I assume that my a-axis/xC is aligned with xL, then my Euler angles would be [0 .226 0]. However, I can't assume xC is aligned with xL due to the documentation saying that xC and zC are arbitrary.

I could be overcomplicating things, but I'd like to know exactly what picture EasySpin is working with on each individual spectrum. Any advice?

[gustim]

I share your question. I am working with a similar crystal and am confused.

Based on what I have seen experimenting around, I suspect the xC direction is set along the a-axis. Thus, zC is orthogonal to the crystal's a-b plane which in some crystals is called the c* direction.

I could be completely wrong, but cannot verify my guess since it is buried in the internal code. Any confirmation or correction would be welcome. Thanks.

[Stefan Stoll]

The documentation might be not entirely clear here. You can choose how to define the xC and yC axes relative to your paramagnetic center - this would manifest in how you define the molecular frame relative to the crystal frame.

The relevant code is in `private/sitetransforms.m` and `private/p_crystalorientations` - have a look at it on the EasySpin repo on Github.