[phenixbb] molecular replacement - restricting rotation around a specified orientation

Christine Gee chrgee at gmail.com
Thu Nov 5 17:21:29 PST 2009

Dear Phenix developers,
We have a protein with two sub domains (N-lobe and C-lobe) we are  
trying to solve by MR.  The C-terminal sub domain solves fine (TFZ  
11.1), but the N-terminal lobe is not being placed correctly.  I read  
in the online documentation that you can specify a limited rotation  
range around the orientation you would expect for the N-lobe based on  
the C-lobe orientation.  My question is, how do specify what  
orientation to start with?  I know I need some Euler numbers, but are  
they just the same ones that the C-lobe writes out with and I use an N- 
lobe that is basically the other half of the C-lobe pdb (ie the X,Y,Z  
co-ordinates are consistent with each other at the beginning of the  
search)? Or do I need to position the N-lobe with the solution C-lobe  
and write it out for use in the search model, and then how do I  
specify the Euler?  Also we were going to try and use normal mode  
perturbation to generate an ensemble and I was wondering if there is  
more documentation somewhere on how to do that?

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