[phenixbb] question on molecular replacement

fn1 at rice.edu fn1 at rice.edu
Sun Jun 10 21:39:15 PDT 2012

Hi Nathaniel,

The crystal reflects to about 2 A. Phenix.xtriage indicates there's no  
twinning. The protein is only 72 aa long by de novo design and we have  
a simulated model. This protein should form a three-helix bundle like  
structure. But i am not pretty sure how accuracy the model is.

Right now i am using phenix.automr to do all the stuff. I don't have  
rosetta installed yet.

Thank you!

Quoting Nathaniel Echols <nechols at lbl.gov>:

> 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
> year.)
> -Nat
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