Hi,
I am currently using relax with the full_analysis.py script.
I face several problems for which I can't find any solution...
1.
With all my data (230 residues at 3 fields, for a total of 2070
observables), the best diffusion model is the local tm. This is not
normal as this protein is globular. Hence, the C-terminus residues have
really high chi2 values... Thus, when excluding the C-terminus, the best
diffusion model is still the local tm. Maybe some other residues are
highly flexible and should be rejected... Maybe also some residues have
bad data... What is a good strategy to find residues I should exclude
from my analysis ?
2.
When I look at optimized results from the ellipsoid runs (second best
choice after local tm), I see lots (~ 50 % residues) of Rex, which is a
bit anoying... The diffusion tensor may not be well optimized... This
may be related to problem 1...
3.
In different situations, some runs (prolate or ellipsoid, i.e. the
diffusion tensor that should best describe my system) never converge and
oscillate between 2 or more AIC values. Some residues oscillate between
2 or more models, but these residues are not special as to their
relaxation data or position in the protein...
Consistency testing and reduced spectral density mapping show that my
data are of good quality and are consistent with each other...
I tried with different structures (crystal structure with added protons,
MM snapshots), but always got the same kind of results...
I tried several hybrids (with no C-ter, with no C-ter and several loops,
etc), but always got the same kind of results...
Also, chi2 values are quite high for most residues (5-20 on average)...
What should I do now ? Do you have any idea ?
Thanks a lot for any help or idea !!!!!!!
Exhausted Séb
Full analysis issue