Rigid Body Vs. EOM

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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lilyestr
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Rigid Body Vs. EOM

#1 Post by lilyestr » 2011.03.22 00:58

Hi everyone,
I have been working on optimizing my EOM models in an attempt to try to understand a conformational change. The protein has several domains with flexible linkers between them. I came across the fact that because constant subtraction between SASREF and Gajoe works differently, I am essentially fitting the models to two slightly different structures. (I am attaching a picture).
I was just wondering what others thought of this, and what your opinions are.
1) Is the difference negligible?
2) Should I even use EOM?
3) Any other thoughts?
In the picture
exp1 is my eom constant substracted data
exp2 is my sasref constant substracted data.
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eom_vs_rigid.jpg
eom_vs_rigid Comparison
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Alex
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#2 Post by Alex » 2011.03.23 19:08

Hi
both fits look good to me. Can you post a Kratky plot?

I think there is an option to switch constant subtraction (at least in EOM).

HTH
Alex

lilyestr
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#3 Post by lilyestr » 2011.03.23 21:45

Hi Alex,
Here is the Krakty plot. By no means is it completely disordered. But we do have evidence of internal flexibility by many several biochemical methods.
I am leaning towards the EOM analysis since a smaller constant is subtracted and the fit is equal if not a little better in some cases. But if you have any other suggestions please let me know!
Thanks,
--Wayne
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Alex
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#4 Post by Alex » 2011.03.23 21:47

Hi Wayne

Tell EOM to select only 3 models per ensemble. Try the same with 1.
Do you get good fit?

HTH
Alex

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