[phenixbb] Incorrect secondary structure assignment in a .pdb
ricardorighetto at gmail.com
Thu Jun 28 13:43:46 PDT 2018
An example of Phenix tool that does not preserve HELIX/SHEET records is
phenix.ready_set (I have version 1.13-2998). Is this a bug or normal
behavior? (apologies for getting slightly off topic)
And thanks for clarifying about the behavior of secondary structure
restraints in phenix.real_space_refine!
Ricardo Diogo Righetto
2018-06-28 22:26 GMT+02:00 Maciej Jagielnicki <mjj5qk at virginia.edu>:
> 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
>> 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.
>> 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:
>> 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
>>> On Thu, Jun 28, 2018 at 12:38 PM, Pavel Afonine <pafonine at lbl.gov>
>>>> Hi Maciej,
>>>> please have a look at item #10 and Notes section here:
>>>> 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!
>>>> 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...
>>>> 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
>>> phenixbb at phenix-online.org
>>> Unsubscribe: phenixbb-leave at phenix-online.org
> 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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