Hi Mohammad,
I do not know if PyMOL can do what you want. But...
If you know how to refine using phenix*, and the pdb has electron density
data, I suggest to refine and validate your structure. In the validation
window, there is specific tab where one can see if the structure has
missing atoms.
If you do not know how to use phenix then you can use pdb-redo** Paper
here***
Good luck
* https://www.phenix-online.org/download/ tutorials @ youtube
** https://pdb-redo.eu/
*** https://pdb-redo.eu/publications/bioinformatics.pdf
El mar., 31 de jul. de 2018 a la(s) 09:24, Mohammad Goodarzi (
mohammad.goda...@gmail.com) escribió:
> Hello,
>
> I would like to know how to check for missing or broken part of a PDB file
> using pymol?
> should i screen within each amino acid or there is a way to show it by
> pymol?
>
> Thanks
> Mohammad
>
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