Hi,
The only differences in the analysis should be due to different bond
orientations. The PDB reference frame doesn't matter - this will only
change the values Euler angles of the diffusion tensor and nothing
else. So if the same structure exists in two different PDB frames,
then the difference in the optimised Euler angles will be solely due
to the rotation between the two structures. If you were to change the
PDB frame in any of your files, the final chi-squared value should be
identical to a non-rotated PDB. The differences you do see are
because the relative XH bond orientations in the different structures
are different.
Regards,
Edward
On 8/30/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
Hi,
I am doing different tests with the full_analysis.py script, data at
three magnetic fields and different PDB structures (taken from MD
simulations).
I realized that those different structures give rise to different
optimization times and also to different chi-squared values for the
different diffusion tensors (I have only tried the prolate diffusion
tensor).
I wonder if the structures need to be processed before giving as inputs
for relax. Especially, do the structures need to be centered relative to
their inertia tensor (like with the pdbinertia program that one should
use prior to model-free analysis using ModelFree).
Thanks !
Sébastien :)
--
______________________________________
_______________________________________________
| |
|| Sebastien Morin ||
||| Etudiant au PhD en biochimie |||
|||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne |||||
|||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
||| 1-418-656-2131 #4530 |||
|| ||
|_______________________________________________|
______________________________________
_______________________________________________
relax (http://nmr-relax.com)
This is the relax-users mailing list
relax-users@xxxxxxx
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-users
Re: PDB orientation