[phenixbb] Incorrect secondary structure assignment in a .pdb

Ricardo Righetto ricardorighetto at gmail.com
Thu Jun 28 13:10:23 PDT 2018

Hi Maciej,

If the PDB file has no secondary structure assignments defined in the
header and you open it in Chimera, it automatically runs ksdssp in the
background to assign helices and sheets, which may or may not be correct
and might make you think that you have secondary structure records in the
header when you actually have nothing:

If in turn you save the PDB from Chimera with such automatically generated
assignments, the records corresponding to this assignment will be written
to the header. And if it's written in the header, by default
phenix.real_space_refine will use these restraints.

Bottom line is that throughout modelling and refinement you should always
inspect your output PDB file from whatever program you use (PHENIX, Coot,
Chimera, etc) to make sure that the information you think should be in the
header is indeed there. I agree that some programs might unnecessarily "get
rid" of the secondary structure records in the header and this is a bit

Hope this helps,

Ricardo Diogo Righetto

2018-06-28 20:02 GMT+02:00 Maciej Jagielnicki <mjj5qk at virginia.edu>:

> 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_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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