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

Randy J. Read rjr27 at cam.ac.uk
Fri Nov 6 04:50:48 PST 2009


At the moment, those are things that you can't do within the Phenix 
interface. Within a month or two (thanks to work that Airlie McCoy and Nat 
Echols are doing), there will be a new GUI that will allow all options of 
Phaser to be used within Phenix.

Presumably you don't want to wait that long! So, in the meantime, you can 
use command scripts or use the ccp4i interface to run the version of Phaser 
distributed with CCP4. I think the documentation on our web-page should be 
reasonably clear for your first question but, if you run into problems, 
please get in touch off-line. Basically, for the ROTATE AROUND search, you 
start with an N-lobe in the orientation it should be in to interact with 
the original C-lobe, then you find orientations near the angle that is 
applied to the C-lobe in your partial solution. In other words, your first 
option should work.

For normal modes, you run a separate normal modes job to write out the 
perturbed structures. It also writes out a ".sol" file that defines the 
ENSEMBLEs corresponding to each of the structures, and SEARCH commands to 
tell Phaser to search with each of these as alternatives. You can then 
include that in your script to run automated MR with each of the perturbed 
structures (with a command like "@nma.sol"). If you're using the ccp4i GUI, 
you can include this .sol file as if it defined a previous partial solution 
but then (if I remember correctly -- I'm in Japan at the moment) you have 
to use the "Run&View Com File" command to edit the automatically-generated 
command script, which will have an extra SEARCH command in it.


Randy Read

On Nov 6 2009, Christine Gee wrote:

>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?
>phenixbb mailing list
>phenixbb at phenix-online.org

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