SUPCOMB it self can be used for publish?

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA
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Donghyuk Shin
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SUPCOMB it self can be used for publish?

#1 Post by Donghyuk Shin » 2013.04.12 17:29

I have just entered SAXS world.
I've analysed data with GNOM, and got .out file. Then, I've made initial model by using DAMMIF.
After this, I just superimposed my crystal structure model with dammif output pdb by SUPCOMB.

And, I've read the SUPCOMB manual, and It said tha "ideally similiar object results in 0 value of NSD"

Here are my question,

1) Where can i find NSD? I think the values at "TRANSFORMATION MATRIX" are the NSD, and is it correct?
2) Can I write down "Crystal structure model is superimposed to SAXS envelope with SUPCOMB(EMBL), and It fits well (NSD=0.5)" for publish?

or do I have to do SASREF to get chi^2 value for evaluating the correlation?

Thanks,

franke
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Re: SUPCOMB it self can be used for publish?

#2 Post by franke » 2013.04.12 19:25

From the subcomb manual:

Code: Select all

                                Initial       Final
              Orientation      Distance    Distance
             1     1     1       1.8697      1.8068
             1     1    -1       1.8335      1.7153
             1    -1     1       2.0625      1.5156
             1    -1    -1       2.0227      1.5015
            -1     1     1       1.8634      1.7839
            -1     1    -1       1.8863      1.7393
            -1    -1     1       2.0400      1.4981
            -1    -1    -1       2.0712      1.5049
Here, Initial and Final distances are the NSD values before and after the minimization.
Besides, the NSD should also be mentioned in the resulting pdb.

For supcomb, please cite: M.Kozin & D.Svergun (2001) Automated matching of high- and low-resolution structural models J Appl Cryst. 34, 33-41. (but don't forget to cite DAMMIF and GNOM).

P.S. Did you run a single model only? You may want to run 10-20 and refine them via damaver/dammin - see the manuals.

Donghyuk Shin
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Posts: 9
Joined: 2013.04.12 13:58

Re: SUPCOMB it self can be used for publish?

#3 Post by Donghyuk Shin » 2013.04.13 01:58

Thank you!
I just run it once, and now I should run SUPCOMB again.
Of course, I should cite GNOM, DAMMIF also.

Thanks a lot! :)

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