[phenixbb] Incorrect secondary structure assignment in a .pdb
Pavel Afonine
pafonine at lbl.gov
Thu Jun 28 13:49:18 PDT 2018
It is a bug. Thanks for letting us know!
Pavel
On 6/28/18 13:43, Ricardo Righetto wrote:
> Dear Pavel,
>
> 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!
>
> Best wishes,
>
>
>
>
>
>
> --
> Ricardo Diogo Righetto
>
> 2018-06-28 22:26 GMT+02:00 Maciej Jagielnicki <mjj5qk at virginia.edu
> <mailto: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).
>
> Maciej
>
> On Thu, Jun 28, 2018 at 4:16 PM, Pavel Afonine <pafonine at lbl.gov
> <mailto: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
>> <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 <mailto: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 <mailto: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
>> <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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>>
>
>
>
>
> --
> Maciej Jagielnicki, MS.
> Graduate Student
> University of Virginia
> Molecular Physiology and Biological Physics
> 480 Ray C Hunt Drive Rm 320
> <https://maps.google.com/?q=480+Ray+C+Hunt+Drive+Rm+320+Charlottesville,+VA&entry=gmail&source=g>
> Charlottesville, VA
> <https://maps.google.com/?q=480+Ray+C+Hunt+Drive+Rm+320+Charlottesville,+VA&entry=gmail&source=g>
> Lab Phone: 434-243-2520
>
>
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