[phenixbb] Incorrect secondary structure assignment in a .pdb

Paul Emsley pemsley at mrc-lmb.cam.ac.uk
Thu Jun 28 14:14:41 PDT 2018


On 28/06/18 17:23, Maciej Jagielnicki wrote:
>
>
> I used a combination of phenix real space refine and Coot to build a
> model into a cryoEM density map. I used an existing .pdb file as a
> starting point for my building. During the build, some helical
> elements became strands and vice versa (it was very clear to my eyes).
> Unfortunately, neither Phenix nor Coot would automatically update the
> header information for secondary structure elements

FYI, Coot indeed won't update the header information for secondary
structure elements automatically. However you can use Coot to update or
generate it

add_header_secondary_structure_info(imol)

Regards,

Paul.



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