[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?
Regards
Christine
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