Re: [ccp4bb] Help with pseudosymmetry problem

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

Previous message:
Subject: Re: Help with pseudosymmetry problem
From: Claudine MAYER mayer {- at -} CHUPS {- dot -} JUSSIEU {- dot -} FR
Date: 2008-04-23

Next message:
Subject: Re: Help with pseudosymmetry problem
From: Alexei Vagin alexei {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-04-23

Subject: Re: Help with pseudosymmetry problem
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-04-23

1) It is a bit hard to find out how MOLREP defines its orthogonal axes -
many programs use X0

a, Yo

b* and in P21 hence Zortho is

to c*
If that is what Molrep does then your 2 fold is in the a c* plane, 21
degrees or 111 degrees from c*.
The 2 peaks you see are symmetry equivalents.

If you draw some slugs related by one of those two folds, then add slugs
generated by the crystallography 21 axis, you will see that you always
must have a 2 fold at theta and also one at theta + 90

( Have I been here before?? Yes! )

As for the Patterson - what height are those peaks relative to the origin?

With 2 dimers in the asymm unit and with the non-cryst 2-fold
perpendicular to b* you could have such translations between one monomer
and another.
is there a model - easiest to solve it then analyse this sort of stuff
later!
Eleanor

Derek Logan wrote:
> Hi everyone,
>
> Can anyone help me with interpretation of a self rotation function and
> native Patterson from a dataset with pseudosymmetry? I've always been
> a bit poor on spherical polars. The space group is P21 with beta =
> 92.2°. The kappa=180° section of the SRF, calculated using Molrep, is at
>
> http://mole.mbfys.lu.se/~derek/selfRF_180.png
>
> and contains two big peaks around 7 sigma. I'm having trouble
> identifying these in the list of peaks from Molrep:
>
> theta phi chi alpha beta gamma
> Isym_i Isym_j
> Sol_RF 1 0.00 0.00 0.00 0.00 0.00 0.00 1 1
> Sol_RF 1 90.00 -90.00 180.00 0.00 180.00 0.00 1 2
> Sol_RF 1 90.00 90.00 180.00 0.00 180.00 0.00 2 1
> Sol_RF 1 0.00 0.00 0.00 0.00 0.00 0.00 2 2
> Sol_RF 2 158.56 180.00 180.00 0.00 42.89 -180.00 1 1
> Sol_RF 2 111.44 0.00 180.00 -180.00 137.11 0.00 1 2
> Sol_RF 2 111.44 0.00 180.00 180.00 137.11 0.00 2 1
> Sol_RF 2 21.44 0.00 180.00 180.00 -42.89 0.00 2 2
> Sol_RF 3 165.65 0.00 180.00 -180.00 28.70 0.00 1 1
> Sol_RF 3 104.35 -180.00 180.00 0.00 151.30 180.00 1 2
> Sol_RF 3 104.35 180.00 180.00 0.00 151.30 -180.00 2 1
> Sol_RF 3 14.35 -180.00 180.00 0.00 -28.70 180.00 2 2
>
> It seems to me to be two copies of peak 2. I believe theta starts in
> the middle, perpendicular to the page and phi starts on the x axis,
> thus the peak just below the centre would be (21.44, 0, 180). I
> presume that the second peak is the symmetry-related (158.56, 180, 0)?
> However where is (111.44 0 180)? I would expect to see this near the
> bottom of the plot, but it's not there. I'm sure I'm missing something
> fundamental about the symmetry of the SRF projection, but
> unfortunately I don't have a supervisor to bug about this (I *am* the
> supervisor...)
>
> In the native Patterson
>
> http://mole.mbfys.lu.se/~derek/nativePatterson.png
>
> there are two peaks of almost equal height. How can this be reconciled
> with having only one strong peak in the SRF? There are most likely two
> dimers in the asymmetric unit, but there may only be one, with very
> high resulting solvent content. What's more the molecules are
> leucine-rich repeat proteins and have weak internal symmetry. I
> believe this was an issue with the ribonuclease inhibitor, but looking
> briefly at the crystallisation article and structure article I wasn't
> able to find a rationalisation of this problem. The 2-fold is
> perpendicular to b*. How could this cause the two peaks?
>
> Thanks
> Derek
>
>
>

CCP4bb navigation

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

Previous message:
Subject: Re: Help with pseudosymmetry problem
From: Claudine MAYER mayer {- at -} CHUPS {- dot -} JUSSIEU {- dot -} FR
Date: 2008-04-23

Next message:
Subject: Re: Help with pseudosymmetry problem
From: Alexei Vagin alexei {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-04-23