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Re: [ccp4bb] tricky molecular replacement |
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CCP4bb navigationCCP4bb <-- 2007 <-- November 2007 <-- 04 November 2007Subject: Re: tricky molecular replacement From: Jan Abendroth jan {- dot -} abendroth {- at -} GMAIL {- dot -} COM Date: 2007-11-04 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 > > 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 ... > CCP4bb navigationCCP4bb <-- 2007 <-- November 2007 <-- 04 November 2007 |
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