Re: [ccp4bb]: MR

[Bart Hazes <bhazes@ualberta.ca>]

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Yes that should work. In the old XPLOR/CNS you could specify your rotations
explicitly and I guess that is still true. You'll have to find out the
direction of your rotation and then rotate around it in lets say 2.5 degree
steps. I hope the scripting language allows you to rotate around a defined
axis. I think you should be able to use the kappa phi psi definition where
kappa is your rotation angle and phi psi should correspond to the vector
between your zinc atoms with the search model superimposed on the zincs in
your experimental structure

An alternative is to generate the set of models yourself and use each one of
them for a translation search in for instance amore. This will require
a bit of scripting but could be more sensitive. If you tell amore not to
translate/rotate your molecule during the tabling step then the correct
solution should have a low R-factor/high correlation and the translation
should be close to zero (since the model is already at the right position).

Since you don't really have to solve the translation problem (you did that by
superimposing) you can also just calculate the agreement, R-factor and
correlation, between Fcalc and Fobs for each of the rotated models.

The real question is whether a successful solution of this problem is going to
give you an interpretable map. At < 30% identity and only 50% of the full
structure I think that's going to be tough. So better to start thinking about
derivatives/Se-Met right away. While doing so you can try to solve this MR
problem, it will at least help you with model building.

Bart

On Fri, 20 Jul 2001, Jeroen Mesters wrote:

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>
> Hi ccp4bb community,
>
> our protein contains two zinc ions for which we are able to pick up
> the signal. However, the phasing power is to low to solve the structure.
> With MR we also failed because the search model is less then half of
> the molecule with about 30 % seq. identity but also containing two zincs.
>
> Is it possible to use the zinc ions as an anchoring point and rotate the
> search model around this axis?! Which program will do so?
>
> THANX, JEROEN
> --
>
> 9. International Conference on the Crystallization of Biological Macromolecules
> http://www.conventus.de/iccbm9/
>
> --
> Jeroen Raymundus Mesters, Ph.D.                           Alias Geronimo
> Dept. of Structural Biology and Crystallography,  Institute of Molecular
> Biotechnology, P.O.Box 100 813, D-07708 Jena, Germany.
> Tel: +49-3641-656063, Fax: +49-3641-656062, E-mail: jmesters@imb-jena.de
> http://www.imb-jena.de/www_sbx/home.html
> --
> If you can look into the seeds of time and say
> which grain will grow and which will not - speak then to me    (Macbeth)
> --
>

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