One other idea idea:
1. Solvent flattening on the hexagonal crystal
2. use the flattening mask to cut out the density of one molecule,
put in a large P1 cell for calculating structure factors
3. Use the structure factors from the density of the hexagonal crystal
to solve the triclinic crystal by molecular replacement.
4. If 3 works, multicrystal averaging to improve both crystals
til the map is traceable.
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 ...
