If you take a PDB file from the solution for the hexagonal form as your
input model for a translation search in P1, then the cross-rotation peaks
that rotate the hexagonal data onto the P1 data should be the correct
orientations. (Phaser uses the same definition for Euler angles as ALMN.)
I'd give a generous list of orientations, because the translation searches
are very fast. These should include symmetry equivalent cross-rotation
peaks, because there's only one copy of the model and you don't know which
symmetry-related orientation to apply to that one.
What you would like to see (apart from a clear solution!) is that the two
orientations are related by the same rotation that you see in the P1
self-rotation function.
Randy Read
On Nov 3 2007, Jan Abendroth wrote:
Hi all,
I have a tricky molecular replacement case. One protein in two different
crystal forms: hexagonal with 1 mol/asu, triclinic with 2 mol/asu (based on
packing and self rotation).
No experimental phases are available this far, however, there is a
distant homology model. For the hexagonal crystals, phaser gives a
solution with really good scores (Z > 9, -LLG > 50) and a good packing.
While the correct solution is way down the list in the RF, the TF can
separate it from the bulk of bad solutions. Slight changes in the model
give the same solution. Maps are somehow ok, however, not good enough to
enable arpwarp to build the model. It does not totally blow up either.
For the triclinic crystal form with 2 molecules related by a two-fold which
is not parallel to a crystal axis, phaser does not find a solution. Neither
does molrep using the locked rotation function with the two-fold extracted
by the SRF.
As the homology between the data set should be higher than between the
model in the data sets and the search model, I tried a cross rotation
function between the two data sets. Strong peaks there should give the
relation between the orientation of the molecule in the hexagonal crystal
(that I believe I can find). With two rotations known and one translation
undefined, I'd be left with only one translation that needs to be found.
Then averaging within P1 or cross crystal might improve the density...
Almn appears to be the only program in ccp4 that can do a cross rotation
using Fs only, right?? I used the P1 data as hklin, the hexagonal data as
hklin2. Almn comes back with two strong peaks (see below), however, now I
am lost: - the first two peaks appear to be the same - are the Euler
angles the ones I could use in a peak list for eg. Phaser? - does this
procedure make sense at all? - any other ideas?
Thanks a lot
Jan
almn.log:
##########
Peaks must be greater than 2.00 times RMS density 52.2161
Eulerian angles Polar angles
Alpha Beta Gamma Peak Omega Phi
Kappa Direction cosines
PkNo Symm: 1 2
Peak 1
1 1 1 323.7 143.4 18.5 540.8 92.9 62.6
143.8 0.4594 0.8867 -0.0511
1 1 2 323.7 143.4 78.5 540.8 83.2 32.6
145.9 0.8364 0.5351 0.1184
1 1 3 323.7 143.4 138.5 540.8 75.6 2.6
157.2 0.9674 0.0441 0.2495
1 1 4 323.7 143.4 198.5 540.8 71.9 332.6
174.4 0.8439 -0.4373 0.3108
1 1 5 323.7 143.4 258.5 540.8 107.2 122.6
167.0 -0.5149 0.8049 -0.2950
1 1 6 323.7 143.4 318.5 540.8 101.7 92.6
151.7 -0.0446 0.9781 -0.2034
1 1 7 143.7 36.6 41.5 540.8 161.7 321.1
175.0 0.2448 -0.1974 -0.9493
1 1 8 143.7 36.6 341.5 540.8 20.4 171.1
128.2 -0.3451 0.0540 0.9370
1 1 9 143.7 36.6 281.5 540.8 31.6 201.1
73.8 -0.4882 -0.1885 0.8521
1 1 10 143.7 36.6 221.5 540.8 82.2 231.1
37.0 -0.6220 -0.7711 0.1363
1 1 11 143.7 36.6 161.5 540.8 144.3 261.1
65.1 -0.0902 -0.5770 -0.8118
1 1 12 143.7 36.6 101.5 540.8 158.6 291.1
118.5 0.1317 -0.3411 -0.9307
Peak 2
2 1 1 143.7 36.6 41.5 540.8 161.7 321.1
175.0 0.2448 -0.1974 -0.9493
2 1 2 143.7 36.6 101.5 540.8 158.6 291.1
118.5 0.1317 -0.3411 -0.9307
2 1 3 143.7 36.6 161.5 540.8 144.3 261.1
65.1 -0.0902 -0.5770 -0.8118
2 1 4 143.7 36.6 221.5 540.8 82.2 231.1
37.0 -0.6220 -0.7711 0.1363
2 1 5 143.7 36.6 281.5 540.8 31.6 201.1
73.8 -0.4882 -0.1885 0.8521
2 1 6 143.7 36.6 341.5 540.8 20.4 171.1
128.2 -0.3451 0.0540 0.9370
2 1 7 323.7 143.4 18.5 540.8 92.9 62.6
143.8 0.4594 0.8867 -0.0511
2 1 8 323.7 143.4 318.5 540.8 101.7 92.6
151.7 -0.0446 0.9781 -0.2034
2 1 9 323.7 143.4 258.5 540.8 107.2 122.6
167.0 -0.5149 0.8049 -0.2950
2 1 10 323.7 143.4 198.5 540.8 71.9 332.6
174.4 0.8439 -0.4373 0.3108
2 1 11 323.7 143.4 138.5 540.8 75.6 2.6
157.2 0.9674 0.0441 0.2495
2 1 12 323.7 143.4 78.5 540.8 83.2 32.6
145.9 0.8364 0.5351 0.1184
Peak 3
3 1 1 335.2 54.5 36.5 209.2 78.8 59.3
55.6 0.5006 0.8437 0.1940 ...
Peak 4
4 1 1 155.2 125.5 23.5 209.2 62.8 155.8
179.4 -0.8112 0.3638 0.4579 ...
Peak 5
5 1 1 349.3 53.8 13.0 176.4 87.7 78.2
53.9 0.2051 0.9779 0.0406 ...
