Dammif & crysol

Ab initio modelling: DAMMIF, DAMMIN, GASBOR, MONSA
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lauren
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Dammif & crysol

#1 Post by lauren » 2010.11.20 19:35

Hi
I have a 20kDa dimmer protein, and trying to build a model with DAMMIF,
I run 20 times DAMMIF with P2 symmetry, and average them by using Damaver (NSD listed below).
xxq16-1.pdb !! Reference file
xxq08-1r.pdb !! NSD = 0.613
xxq14-1r.pdb !! NSD = 0.625
xxq12-1r.pdb !! NSD = 0.595
xxq05-1r.pdb !! NSD = 0.520
xxq18-1r.pdb !! NSD = 0.504
xxq13-1r.pdb !! NSD = 0.744
xxq01-1r.pdb !! NSD = 0.719
xxq07-1r.pdb !! NSD = 0.565
xxq02-1r.pdb !! NSD = 0.818
xxq04-1r.pdb !! NSD = 0.852
xxq11-1r.pdb !! NSD = 0.888
xxq09-1r.pdb !! NSD = 0.952
xxq03-1r.pdb !! NSD = 1.057
xxq20-1r.pdb !! NSD = 1.066
xxq15-1r.pdb !! NSD = 1.118
xxq17-1r.pdb !! NSD = 1.161
xxq06-1r.pdb !! NSD = 1.213
xxq21-1r.pdb !! NSD = 1.234
i) Can I use the "damfilt.pdb" as the final envelop model for publication? Or should I further refine with dammin using the damstart.pdb?

ii)The two lines in the dammif output file "xxq16.fit" fit well with each other.
However, when I try to fit the model "xxq16-1.pdb" to my raw data by Crysol, it doesn't fit well. Which one is correct?


Thank you very much for your help,

Lauren

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Hayds
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#2 Post by Hayds » 2010.11.21 10:21

Hi Lauren,

in the .fit file you see the regularised curve from GNOM and the fit to this from the model. The fit to the actual SAXS data is shown in the .fir file. Does this look more like the fit you get when using CRYSOL and one of your models?

Cheers,

Haydyn

lauren
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#3 Post by lauren » 2010.11.22 09:22

Thanks!
The .fir looks more like the fit I get in CRYSOL. :lol:
But still a little bit confused,
It seems that the model fit to the GNOM data(.fit), but the model does't fit to the raw data(.fir). Is that mean my GNOM file doesn't fit my raw data(It do "fit" when I running GNOM)? And what should I do next?

Kind Regards
Lauren

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Hayds
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#4 Post by Hayds » 2010.11.22 10:03

Hi Lauren,

It's hard for me to say unless I see the data and the P(r) function. Is it possible to post the saxs profile, p(r) function and .fit/.fir files? You can always PM me if this is a problem.

Cheers,

Haydyn

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AL
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#5 Post by AL » 2010.11.22 18:57

lauren wrote:However, when I try to fit the model "xxq16-1.pdb" to my raw data by Crysol, it doesn't fit well.
CRYSOL is designed to evaluate the scattering from macromolecules with known atomic (high resolution) structure (and fit it to experimental data); it is incorrect to use it on dummy atom models (unless you specify zero solvent density).
Hayds wrote:You can always PM me if this is a problem.
Private messaging has been disabled on this board to avoid spam attacks.
Last edited by AL on 2010.11.24 20:54, edited 1 time in total.

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Hayds
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#6 Post by Hayds » 2010.11.22 19:28

AL wrote:CRYSOL is designed to evaluate the scattering from macromolecules with known atomic (high resolution) structure (and fit it to experimental data); it is incorrect to use it on dummy atom models
Yep, that's true. We have a utility called pdb2alm for this. Al, is it in the downloadable ATSAS 2.4 package?

h

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pdb2alm

#7 Post by AL » 2010.11.23 01:27

I don't think it is in the package - normally one does not need to recalculate the curve since it is contained in the fit/fir files.

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Ultimate DA model

#8 Post by AL » 2010.11.23 16:41

lauren wrote:Can I use the "damfilt.pdb" as the final envelop model for publication? Or should I further refine with dammin using the damstart.pdb?
Provided that you had a decent p(r) function and the fir looks good, based on your NSD values I would use xxq16-1.pdb for publication.

lauren
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#9 Post by lauren » 2010.11.24 16:06

Thanks for all your reply, Really helpful :D

After I cut down a little bit resolution (q range 3.5->3.0).
The .fir and .fit looks fit now.:D
Three picture belows show my new process data and the pr function, and also the old one, (which I do change the alpha value to make two curve fit together, I don't know if it is the reason?, or simply it is not good?)

Kind Regards

Lauren
Attachments
newfit.png
new process data
newfit.png (25.5 KiB) Viewed 7517 times
newpr.png
new p(r) function
newpr.png (28.42 KiB) Viewed 7517 times
old_pr.png
old p(r) function
old_pr.png (27.69 KiB) Viewed 7517 times

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