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Re: [ccp4bb] tricky molecular replacement
 

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CCP4bb <-- 2007 <-- November 2007 <-- 05 November 2007
Previous message:
Subject: refmac5: FIND CONTACT WITH BRICKING failed
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-11-05 		Next message:
Subject: Re: tricky molecular replacement
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-11-05


Subject: Re: tricky molecular replacement
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-11-05
Yes- ALMN seems to have given one excellent match between the data sets
which is encouraging.
But since you are matching hexagonal to trigonal you get a large number
of symmetry equivalent peaks, relating a molecule from the P1 set to one
of the hexagonal set.
The angles are defined so that:
"The rotation given by the angles of a peak rotates
coordinates in the orthogonal frame of crystal 2 to
the orthogonal frame of crystal 1."

You are right that cross crystal averaging can help
Do you have a dimer in the hexagonal form - maybe generated by crystal
symmetry?
I would check whether that dimer axis is rotated by any of the solutions
for Peak 1 to lie along the NCS two-fold of the P1 form, then try
refining that dimer in the P1 cell.

( A tip: add 2 phoney coordinates to your model that sit on the 2 fold
axis, maybe 0 0 0 and 0 0 1 of course ) then see where they finish up
after you apply the rotations
Eleanor


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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CCP4bb <-- 2007 <-- November 2007 <-- 05 November 2007
Previous message:
Subject: refmac5: FIND CONTACT WITH BRICKING failed
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-11-05 		Next message:
Subject: Re: tricky molecular replacement
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-11-05


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