# [MMTK] point group symmetry

**Margot Ernst
**
margot.ernst@univie.ac.at

*Thu, 6 Jun 2002 09:54:54 +0200*

Hi Konrad,
thanks for your replies. I have certainly made sure that pairs of degener=
ate=20
modes are included as pairs, and I wonder which point I'm not getting: Th=
e=20
picture I get this far is as follows: the proteins consist of five (ident=
ical=20
or similar) subunits, 200some residues each. I calculated the following s=
ets=20
of modes: 222, 486 and 612., keeping modes 7 to 16 for analysis. The orde=
ring=20
of the modes (in terms of their average deformation energy) and the lowes=
t=20
average deformation energy are *quite* different from each set to the nex=
t,=20
with the lowest mode being at around 700 (612 modes) up to 1000 (222 mode=
s).=20
With low coarseness and high deformation threshold, using up to 4 modes, =
I=20
get nearly symmetrical domains, but as I increase c ( 10 and larger) the=20
symmetry gets lost dramatically. So, after my first mail I was in fact ab=
le=20
to find reasonably symmetrical domains, but I fail to understand why the=20
symmetry gets lost totally at higher c.=20
This far, including up to 4 modes and fine-tuning the c and def.th. valu=
es I=20
see what I expect to see, if I try and include more modes (in the hope to=
get=20
more information into the clustering process) I no longer find a def.=20
threshold that gives domains with proper symmetry (and I mean they are=20
*totally* asymmetrical). When the lowest mode I include has an average de=
f.=20
energy of 700 and the highest is at 2500 the domains do not appear to bre=
ak=20
into larger and smaller contributions, but they simply get lost. Any=20
suggestions beyond trying with a lot more calculated modes? (hope I'm not=
=20
being tedious)
margot