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 <[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 ...
>>>
>
>
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