The procedure of cutting out electron density, putting it into a large unit
cell, and backtransforming to get structure factors can be tricky (as
you've discovered), so we put some instructions on our webpage:
http://www-structmed.cimr.cam.ac.uk/phaser/density_as_model.html
The last time I tried that it worked, but let me know if you run into any
problems with your case.
Randy Read
On Nov 4 2007, 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 ...
