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Re: [ccp4bb] tricky molecular replacement |
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CCP4bb navigationCCP4bb <-- 2007 <-- November 2007 <-- 05 November 2007Subject: Re: tricky molecular replacement From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2007-11-05 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 > >> 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 <-- 05 November 2007 |
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