two questions: hybrid analysis and convergence problems -- June 24, 2007 - 19:13

Hi All,

I have two separate but related questions.  I am using relax 1.2 (svn  
version 3301).  I have relaxation data collected at two fields -- 500  
and 600 MHz.  However, I have data for 9 additional residues at 600  
MHz that were unresolved at 500 MHz.

(1)  The protein I am studying has two domains, with considerable  
interactions between them, connected by a flexible linker.  When all  
data (domains + linker) was included in the calculations, the  
full_analysis.py protocol picked local_tm for the AIC selection of  
the diffusion tensor.  I would like to analyze my data using a hybrid  
model:  (a) the two domains together (using the same diffusion  
tensor) and (b) the flexible linker using a separate diffusion tensor  
(likely local_tm).  My guess is that a prolate or oblate tensor will  
be selected for the domains when analyzed without data from the  
linker region (the quadric_diffusion program from Art Palmer suggests  
an axially symmetric tensor is a good approximation).

Can anyone provide an example of a script where relax is used to  
analyze a hybrid model, or briefly outline the steps?  For example,  
should I run a local_tm optimization using all residues, then  
unselect the flexible linker residues in the unresolved file (as  
specified in the full_analysis.py script) and continue the  
optimization of the other tensors (sphere, prolate, oblate and  
ellipsoid)?


(2)  I am currently running the full_analysis.py protocol, without  
the data for the linker region.  The optimization of the prolate  
tensor is taking much longer than the other tensors for this  
calculation (currently on round_30), as well as the prolate  
calculation using all data including the linker region (it converged  
in 14 rounds).  The differences in the parameters between rounds are  
very small:

"""
#####################
# Convergence tests #
#####################


Chi-squared test:
    chi2 (k-1): 785.88714033105236
    chi2 (k):   785.88714033128417
    The chi-squared value has not converged.

Identical model-free models test:
    The model-free models have converged.

Identical parameter test:
    Parameter:   tm
    Value (k-1): 6.794068350295769e-09
    Value (k):   6.7940683502957698e-09
    The diffusion parameters have not converged.

    Parameter:   Da
    Value (k-1): 6337661.7164024841
    Value (k):   6337661.7164041474
    The diffusion parameters have not converged.

    Parameter:   theta
    Value (k-1): 1.6904048161417038
    Value (k):   1.6904048161417222
    The diffusion parameters have not converged.

    Parameter:   phi
    Value (k-1): 0.30710640562938446
    Value (k):   0.30710640562950142
    The diffusion parameters have not converged.

"""

relax does not report a problem for a specific residue, as was  
reported in the following post (https://mail.gna.org/public/relax- 
users/2006-12/msg00002.html).  Could this be a result of having data  
at only one field for the 9 residues?

Thanks in advance,

Doug