Re: [ccp4bb] tricky molecular replacement

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: opinion : phaser RMSD vis-a-vis LLG, Z-score
From: "Randy J {- dot -} Read" rjr27 {- at -} CAM {- dot -} AC {- dot -} UK
Date: 2007-11-03

Next message:
Subject: Re: opinion : phaser RMSD vis-a-vis LLG, Z-score
From: "Randy J {- dot -} Read" rjr27 {- at -} CAM {- dot -} AC {- dot -} UK
Date: 2007-11-03

Subject: Re: tricky molecular replacement
From: "Randy J {- dot -} Read" rjr27 {- at -} CAM {- dot -} AC {- dot -} UK
Date: 2007-11-03

If you take a PDB file from the solution for the hexagonal form as your
input model for a translation search in P1, then the cross-rotation peaks
that rotate the hexagonal data onto the P1 data should be the correct
orientations. (Phaser uses the same definition for Euler angles as ALMN.)
I'd give a generous list of orientations, because the translation searches
are very fast. These should include symmetry equivalent cross-rotation
peaks, because there's only one copy of the model and you don't know which
symmetry-related orientation to apply to that one.

What you would like to see (apart from a clear solution!) is that the two
orientations are related by the same rotation that you see in the P1
self-rotation function.

Randy Read

On Nov 3 2007, 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 <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: opinion : phaser RMSD vis-a-vis LLG, Z-score
From: "Randy J {- dot -} Read" rjr27 {- at -} CAM {- dot -} AC {- dot -} UK
Date: 2007-11-03

Next message:
Subject: Re: opinion : phaser RMSD vis-a-vis LLG, Z-score
From: "Randy J {- dot -} Read" rjr27 {- at -} CAM {- dot -} AC {- dot -} UK
Date: 2007-11-03