Re: [ccp4bb]: Trouble in interpreting self-ratation map...

[M.Isupov@exeter.ac.uk]

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Dear Woo-Cheol Lee,

>Although this may not be related to CCP4, I need your advice
>on the following puzzle.
Most probably CCP4 BB is the best place to discuss such matters.

>(Gel filtration specified it's a hexamer.)
I would not put too much trust in Gel filtration, and your unit cell
can contain more than one oligomer.

>http://www.geocities.com/fakeophelia/self-rotation.gif

Your MOLREP self-rotation map would suggest to me that you have
two tetramers with 222 point group symmetry in your triclinic cell.
These are related by a two-fold NCS  axis (MAIN DYAD)
located at phi=45, omega=90  for which  the rotatin function value
is higher (RFmax = 5691) than other dyads peaks (Chi=180), which
relate dimers in the tetramers and also  odd peaks at Chi=70.8,
Chi=120 and Chi=146.7 (RFmax about 2000)  which relate dimers of the
two
tetramers which are not related by the MAIN DYAD.


>According to Schroder et al. (Structure, 2000, 8(6):605), they
>created 3,600 search models from the interpretation of self-ratation
>map and solved the structure by MR. How can one create such large
>numbers of probes?

Yes we have generated all 36 hundred decamers in the above paper
using
relatively simple C-shell script and a bunch of CCP4 programs.
I can send you this script  and a script to grep and analyse the
solutions
if you are interested.

Best wishes with your molecular replacement studies.

Misha Isupov,
University of Exeter
>dear CCP4BB readers
>
>Although this may not be related to CCP4, I need your advice
>on the following puzzle.
>
>I have a triclinic crystal of which structure can (hopefully...)
>be solved by molecular replacement. According to matthews-coef
>, the protein is possibly a hexamer(3.0) ~ octamer(2.3).
>(Gel filtration specified it's a hexamer.)
>
>The problem is that I can't imagine the NCS point group by looking
>at the self-rotation map. It has strong peaks at chi=180, 146.7,
119,
>and 70.9. I could find 8 peaks at chi=180. The map itself is
>reachable here.
>
>http://www.geocities.com/fakeophelia/self-rotation.gif
>
>Can someone help me to understand the possible spatial arrangement
>of this multimeric protein?
>
>I have one more question.
>According to Schroder et al. (Structure, 2000, 8(6):605), they
>created 3,600 search models from the interpretation of self-ratation
>map and solved the structure by MR. How can one create such large
>numbers of probes?
>
>Thank you for your help in advance.
>
>Woocheol
>--
>Woo-Cheol Lee
>tel. +81-3-5841-5446 fax. +81-3-5841-8023
>Food Eng. Lab, Univ. Tokyo