[phenixbb] question on molecular replacement

Nathaniel Echols nechols at lbl.gov
Sun Jun 10 21:15:06 PDT 2012

On Sun, Jun 10, 2012 at 7:57 PM,  <fn1 at rice.edu> wrote:
> I have a dataset in P21221. The cell content analysis shows that there
> should be 5 monomers in asu. The gel filtration profile of this protein
> shows that it should form a tetramer.

I agree with Francis - try all possible space groups in the P222 point group.

> I have a simulated structure as searching model. I try to use the whole
> model or backbone model, and different resolution cutoff. When the whole
> model is used, the llg of solution is negative. When the backbone model is
> used, the llg is about 160 when searching for 4 monomers and tfz is 7.4. But
> the following autobuild process could not lower rfactor than 50%.

It would help if we knew more about the properties of the model and
data.  What is the sequence identity of the closest homologous
structure?  Comparative models are often problematic, and those
statistics aren't great.  Also, if the resolution is poor, AutoBuild
isn't going to be able to do much.  This may be a case where
MR-Rosetta is the solution, but I'd verify that you're running the MR
search correctly (and that it has any chance of working to begin with)
before trying that.

> I notice online that it might be useful to run self rotation function first
> to find ncs operators before doing mr. Is this true and how can i do this?

I'm pretty sure CCP4 has a program to do this, but I don't think we
have anything in Phenix yet.  (I suspect it's straightforward to code,
but I couldn't figure out the math when I looked at it briefly last


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