Dear Edward,
Thank you for your help concerning running Relax earlier in the year. I
have now successfully run the full_analysis.py script on two receptors
from different species (ie similar structures, but different binding
affinity to a peptide).
I have a few questions...
1. For each run - sphere, oblate, etc. I had to remove different residues
in order to help the run to finish (I generally removed those that were
fluctuating between two models endlessly) and restarted the run. The runs
went well past fifteen rounds if I didn't do this.
2. Does this mean that I am affecting the final model selection by doing
this? By removing all of the R2/R1/NOE values from a whole loop, I could
be changing how well the model performed. For example this loop could be
more condusive of a spherical model, but with the residues removed,
perhaps an oblate model performs better (although it shouldn't).
3. The obvious answer to this is run all of the models with all the
residue's R1/R2/NOE values left in, but this would take months. It was
taking over a day for each model anyway, so in total around two weeks for
the complete calculation.
4. So - my case, I have two species of the same receptor - human was found
to be oblate and chicken was found to be spherical. I would expect
spherical for both, as the spherical models very well describe what is to
be expected for each receptor and both receptors are very similar in
structure, with chicken only containing three extra residues. Should I
discount the oblate model?
5. Comparing to ModelFree4 results - rigid residues have similar S2
values, but those that are more flexible have much lower S2 values in
Relax than in MF4. Is this simply because Relax has models 6-9 in
addition to the first 5 and so S2 values will be different? For the MF4
results I simply calculated a spherical model, models0-5, at both 600 MHz
and 900 MHz. In Relax I combined them.
I've only been using dynamics programs for 6 months, so if I've missed
something obvious, please let me know. In addition if you would like any
files to look at - just email this address.
Thank you!
Madeleine Strickland
Oblate vs. sphere