[phenixbb] Incorrect secondary structure assignment in a .pdb

Maciej Jagielnicki mjj5qk at virginia.edu
Thu Jun 28 13:26:39 PDT 2018

Thank you for clarification Ricardo and Pavel.

It still amazes me though that different pdb viewers would make such
ridiculous SS predictions/assignments at times for a file that does not
come with that information in the header.
And it seems that during a deposition to PDB I have to manually add the
location of helices/sheets into the .cif files generated by the deposition
system...otherwise I go for deposition somewhat blind (this has of course
nothing to do with Phenix, but adds more to my confusion).


On Thu, Jun 28, 2018 at 4:16 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> The point is that no automated secondary structure (SS) annotation
> software can assign SS fully correctly simply because it relies on input
> model geometry, and models that are subject to refinement are rarely
> perfect for these software to do a great job. This is why the Manual (see
> previous email) recommends getting initial automated assignment first using
> phenix.secondary_structure_restraints (which uses various annotation
> methods, including ksdssp) and then manually checking and editing it if
> necessary.
> Tools within Phenix always preserve HELIX/SHEET records in PDB files. Let
> us know if you have an example where this is not the case.
> Pavel
> On 6/28/18 13:10, Ricardo Righetto wrote:
> 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:
> https://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html
> 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
> annoying.
> 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
>> _______________________________________________
>> phenixbb mailing list
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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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