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
_______________________________________________
relax (http://nmr-relax.com)
This is the relax-users mailing list
[email protected]
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
