[phenixbb] Incorrect secondary structure assignment in a .pdb

[Oleg Sobolev]

Hi Maciej,

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)
>
Can you describe more specifically what exactly the tool you are using? One
way around it would be to convert your pdb to mmcif using
phenix.pdb_as_cif
tool which will preserve SS information.


>  How can you have SS elements displayed if it description is missing from
> the header?
>
As pointed by Ricardo, visualization programs usually can display SS
without any header. On top of that, whether they will use the header if it
is present - also depend on particular program.

Best regards,
Oleg Sobolev.


> 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_sp
>> ace_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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