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,
SUPCOMB it self can be used for publish?
Re: SUPCOMB it self can be used for publish?
From the subcomb manual:
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.
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
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.
-
- Member
- Posts: 9
- Joined: 2013.04.12 13:58
Re: SUPCOMB it self can be used for publish?
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!
I just run it once, and now I should run SUPCOMB again.
Of course, I should cite GNOM, DAMMIF also.
Thanks a lot!
