[phenixbb] Incorrect secondary structure assignment in a .pdb

Oleg Sobolev osobolev at lbl.gov
Thu Jun 28 10:36:31 PDT 2018

Hi Maciej,

I would add that you can obtain recreated SS annotations for your model
phenix.secondary_structure_restraints <your
model> ignore_annotation_in_file=True format=pdb

More on this:

Best regards,
Oleg Sobolev.

On Thu, Jun 28, 2018 at 9:38 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Maciej,
> please have a look at item #10 and Notes section here:
> http://www.phenix-online.org/documentation/reference/real_
> space_refine.html
> 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!
> Pavel
> 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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