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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 <[log in to unmask]> 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 ... >> >