I would stop trying to use a map! that is an act of desperation when you
have uninterpretable but possibly somewhat true experimentally phased
density..
If you have a model it is MUCH MUCH easier!
So as I said - I would find the best hexagonal dimer - you may know this
or you can dispatch the solution to PISA to see what it suggests (
www.ebi.ac.uk/msd/ and look for msdpisa server)
Then search the P1 cell using that dimer and also check out the dimer
rotated by those ALMN angles and I would bet one will be correct..
Eleanor
Jan Abendroth wrote:
Hi all,
thanks a lot for the various responses. When I tried to use a map as the
serach model, I ran into various problems:
again, the starting point is a weak, yet convincing molecular replacement
solution in the hexagonal crystal form (1mol/asu) and no MR solution in P1
(2mol/asu, 2-fold in SRF).
a) using phaser and defining the search model though DM map of the MR
solution in the hexagonal form: Phaser stops as two space groups were used,
p1 for the data set and P6... for the map
b)
- fft to create map after MR and DM of hexagonal form (map in P6..., asu)
- mapmask to cover MR solution (in P6..., asu)
- mapcutting using map and mask from prev steps (P6.., asu)
- sfall to generate FC, phiC in large P1 cell:
"fatal disagreement between input info and map header"
c) same steps as in (b), however, using P6... and full unit cell
- mapcutting: maprot dies with "ccpmapin - Mask section > lsec: recompile"
d) same steps as in (b), however, using P1 throughout
- sfall dies with: "Fatal disagreement between input info and map header"
e) same steps as in (c), however, using P1 and full unit cell - should not
be different from case (d)
- mapcutting: maprot dies with "ccpmapin - Mask section > lsec: recompile"
Any ideas? I btw. use the osx binaries from the ccp4 webpage.
Thanks for any input!
Cheers
Jan
On 11/2/07, Edward A. Berry <[EMAIL PROTECTED]> wrote:
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 ...
