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Hello Misbah--
>
> I am using Python (annealed and refinement) scripts for my structure
> determination. I am new to python scripts/NMR structure determination,
> so I hope they are acceptable annealed structures. Could you please
> clarify the "acceptable annealed" term for me? How can I tell they
> acceptable or not?
Are the experimental and covalent restraints satisfied?
>
> I managed to obtain 200 annealed structures and then carried out
> refinement on one of the lowest RMSD annealed structure. The total
> average RMSD for annealed structures is lower than the total average
> RMSD for my refinement structures. Also the overlay of refined
> structures is not very good as I am getting more than 20 different
> conformations in total of 200 structures. So I was not quite sure
> which one to choose as my final structure...?
do the 20 conformations all satisfy the restraints? Filter out the bad
ones.
The main differences between anneal.py and refine.py are
1) the former starts from random coordinates in torsion angle space (if
you're using the latest version), while refine starts from a given
structure. Older versions of anneal.py started with an extended
structure.
2) the high-temperature dynamics phase is much longer for annealing.
I hope this helps--
Charles
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