[phenixbb] Incorrect secondary structure assignment in a .pdb

Pavel Afonine pafonine at lbl.gov
Thu Jun 28 09:38:11 PDT 2018

Hi Maciej,

please have a look at item #10 and Notes section here:


One sentence summary is: Make sure you use secondary structure (SS) 
restraints in refinement, also making sure you provide SS annotations as 
HELIX/SHEET records in input PDB that are as accurate as possible; this 
is critical for successful refinement.

If you have more questions please get back to us!

Good luck!

On 6/28/18 09:23, Maciej Jagielnicki wrote:
> Hi All,
> 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, and I had to 
> manually edit the header so that helices would show up in correct 
> places when the .pdb file was viewed in Chimera or similar software. 
> Not an ideal way of doing this which is likely related to what 
> happened next.
> When the header information is removed, however, as it happens when 
> the pdb.extract tool prepares a .pdb file for submission by turning it 
> into a .cif file, the secondary structure elements are still displayed 
> when a .cif file is visualized (bizzare in itself) but also the 
> secondary structure is taken straight from the starting .pdb file (the 
> one I used as a base for my model to which there is no connection 
> whatsoever). The question is this - where does the incorrect secondary 
> information come from in the absence of the header? How to fix this? I 
> cannot deposit a file that shows helices/sheets wherever it wants...
> Regards,
> Maciej J.
> -- 
> Maciej Jagielnicki, MS.
> Graduate Student
> University of Virginia
> Molecular Physiology and Biological Physics
> 480 Ray C Hunt Drive Rm 320
> Charlottesville, VA
> Lab Phone: 434-243-2520

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