Hi Edward,
So I've got wild type = oblate chosen, and mutant = ellipsoid chosen.
When you look at the wild type, this gets the strange low values in both
oblate and ellipsoid, but not prolate/sphere. The mutant has beautiful
values in all. I'm wondering whether the wild type data is just not as
good. I might need to go over it - I did it much earlier, so my peak
picking might be wrong. I've found that R1 and NOE values agree very
well, as they should, but R2 are very different - since these experiments
have the largest noise, it may be due to the way I peak picked them - with
the mutant I actually manually peak picked, whereas with the wild type I
didn't I just picked every peak on the same spot, using the peak in the
first delay as a reference. I think the latter technique may help with
the R2 values. Chemical exchange should be similar in both apart from the
mutated loop, where it disappears in the mutant.
I think basically - the two proteins where I manually peak picked I got
the best results, and in the fastest time too, with the fewest rounds.
The two proteins where I didn't worry as much about the T2 data, I got
extremely long calculation times and I ended up having to delete some
residues' data in order to allow the programme to finish. I think it
might be best if I go back and look at the T2 data again and rerun for the
latter two proteins.
Maddy
---------------------------- Original Message ----------------------------
Subject: Re: [Fwd: Re: Extracting results - eg sphere]
From: "Edward d'Auvergne" <edward@xxxxxxxxxxxxx>
Date: Thu, June 16, 2011 8:10 am
To: "Maddy Strickland" <M.Strickland@xxxxxxxxxxxxx>
Cc: relax-users@xxxxxxx
--------------------------------------------------------------------------
Hi,
It is strange that the S2 values are so far off. Are they the same if
you look at both ellipsoids or both prolate spheroids? How do the
diffusion tensors compare? Did you use single-scan interleaving,
temperature compensation blocks, and per experiment MeOH temperature
calibration? Do you see extensive chemical exchange or nanosecond
motions? How did you use relax, and which version of relax are you
using? How do both sets of NOEs compare, is the average identical in
both systems? And are the R1 and R2 averages the same?
For the global models that are not in the 'final' run, it is true that
these have no errors. The reason is that Monte Carlo simulations are
expensive, computationally wise, so they are only used at the very end
once all model selection is performed. You can use relax to calculate
the errors for each model anyway. If you go to the last round_*/opt
directory, you can use a custom script there. Try something like:
# Load the program state.
state.load('state')
# Monte Carlo simulations.
monte_carlo.setup(number=500)
monte_carlo.create_data()
monte_carlo.initial_values()
minimise('newton')
eliminate()
monte_carlo.error_analysis()
# Save the program state.
state.save('state_errors', force=True)
You will have to play with this, as you might have to fix the
diffusion tensor if calculations are far too long. Or there might be
other option you'll need to play with too, but hopefully together with
the relax manual that shouldn't be too hard to work out.
Regards,
Edward
On 15 June 2011 15:06, Maddy Strickland <M.Strickland@xxxxxxxxxxxxx> wrote:
Yes, I want to look at all the different models - sphere/ellipsoid/prolate
etc. to see how S2 values differ. I've got two proteins - one of which is
a mutant of another (only a few residues mutated), but they came out with
different models, one with ellipsoid and one with prolate. When I
compared the S2 values for the two, one was about 0.5 different on every
value (the prolate model was completely off). When looking at the
spherical model it is much closer to what is expected. (I have four
homologous proteins and all are very similar except this prolate model, so
I can't work out why this is so different and I can't work out why it has
been chosen with such strange S2 values. I wanted to compare all four
spherical models instead of using anisotropic ones. I have worked out how
to do this, but unfortunately, I think S2 error and Rex error is
calculated right at the end in the 'final' round as I can't seem to
extract this from 'opt' folders in the final round of 'sphere' or
'prolate' for example.
Any ideas? Is error calculated in each round, or is it calculated right
at the end and therefore impossible to collect for individual
'sphere'/'prolate' etc. that haven't been chosen?
Maddy
---------------------------- Original Message ----------------------------
Subject: Re: Extracting results - eg sphere
From: "Edward d'Auvergne" <edward@xxxxxxxxxxxxx>
Date: Tue, June 14, 2011 10:17 am
To: "Maddy Strickland" <M.Strickland@xxxxxxxxxxxxx>
"Michael Bieri" <michael.bieri@xxxxxxxxxxxxx>
Cc: relax-users@xxxxxxx
--------------------------------------------------------------------------
Hi Maddy,
It should be possible, but you may have to manually modify your
extraction scripts. All of the results files are saved, so all of the
data is there. I'm assuming you'd like to compare the different
diffusion tensor results, is that correct? You will need to choose
which file you look at. Just look through the directories and pick
the final round for each tensor, and go into the 'opt' directory. The
results.bz2 file in that directory will be the one you want. Maybe
Michael can help with the modification of his script, if you are
having troubles.
Regards,
Edward
On 9 June 2011 13:03, Maddy Strickland <M.Strickland@xxxxxxxxxxxxx> wrote:
Hello everyone,
I was wondering if there was a way to extract results, say just from the
spherical folder or just from the ellipsoid folder for example, displayed
as s2.txt, rex.txt etc. like with the final data extraction script, but
for a different model than is selected by the program?
Madeleine Strickland
MCJC Group
N317, School of Chemistry, Bristol University
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Madeleine Strickland
MCJC Group
N317, School of Chemistry, Bristol University
_______________________________________________
relax (http://nmr-relax.com)
This is the relax-users mailing list
relax-users@xxxxxxx
To unsubscribe from this list, get a password
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Madeleine Strickland
MCJC Group
N317, School of Chemistry, Bristol University
Re: [Fwd: Re: [Fwd: Re: Extracting results - eg sphere]]