[phenixbb] Incorrect secondary structure assignment in a .pdb

Maciej Jagielnicki mjj5qk at virginia.edu
Fri Jun 29 08:07:23 PDT 2018


Agreed. Just wanted to make sure I am providing my interpretation of SS
along with just atom coordinates. And got even more confused by the pdb -
to - cif conversions...
Maciej

On Thu, Jun 28, 2018 at 4:47 PM, Christian Roth <christianroth034 at gmail.com>
wrote:

> I wouldn't necessarily say they are ridiculous. If you choose to show a
> cartoon, some viewers run in the background a secondary structure analysis
> program (dssp and variants thereof) and depending on the threshold will
> assign automatically secondary structure elements. None of these automatic
> routines is perfect and even if you do it manually, opinions between
> different people will give a spread in terms of when to draw a helix or how
> long it should be for example. However, no one has to use the provided ss
> definitions in a file. If someone downloads a file from the pdb and
> interprets the structrue might disagree with the boundaries and definitions
> of the secondary structure provided and amend them.
>
> Cheers
> Christian
>
> On Thu, Jun 28, 2018 at 9:27 PM Maciej Jagielnicki <mjj5qk at virginia.edu>
> wrote:
>
>> 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> 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_
>>>>> 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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>
>


-- 
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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