[ccp4bb] tricky molecular replacement

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

Previous message:
Subject: I can't get phaser to build on 10.5
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-11-02

Next message:
Subject: Re: tricky molecular replacement
From: "Edward A {- dot -} Berry" EABerry {- at -} LBL {- dot -} GOV
Date: 2007-11-03

Subject: tricky molecular replacement
From: Jan Abendroth jan {- dot -} abendroth {- at -} GMAIL {- dot -} COM
Date: 2007-11-02

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 navigation

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

Previous message:
Subject: I can't get phaser to build on 10.5
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-11-02

Next message:
Subject: Re: tricky molecular replacement
From: "Edward A {- dot -} Berry" EABerry {- at -} LBL {- dot -} GOV
Date: 2007-11-03