[phenixbb] Incorrect secondary structure assignment in a .pdb

[Maciej Jagielnicki]

Thank you for the suggestion.

Nothing changes when I run phenix real space refinement with SS restraints
turned on. I can either input a .pdb file with correct SS information in
the header or a .pdb file with no SS information at all and the end result
(new refined .pdb) is the same file with the same SS information in a new
header. The information stays the same and 'correct'.

The main problem in my original question is that when I (or the pdb extract
tool that converts a .pdb file to a .cif file for submission to PDB) remove
the header SS information altogether (why you would do that for PDB
deposition is unknown to me), that resulting .pdb file still shows SS
elements in different pdb viewers but SS info is no longer correct. How can
you have SS elements displayed if it description is missing from the
header?
Maciej

On Thu, Jun 28, 2018 at 12:38 PM, 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
>
>
>


-- 
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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