[phenixbb] Incorrect secondary structure assignment in a .pdb
Pavel Afonine
pafonine at lbl.gov
Fri Jun 29 10:29:44 PDT 2018
If you have manual SS annotation (or semi-manual) that you believe is
correct -- keep it. Likely, automatically generated SS annotation is
going to be worse. But if you like jumping between tools then I afraid
you are to live with the fact that all of them have different ideas
about handling SS records.
A tool that may be handy in this context is
phenix.secondary_structure_validation which validates SS records.
Pavel
On 6/29/18 08:05, Maciej Jagielnicki wrote:
> Thanks Oleg,
> I was using the 'pdb extract' online tool provided by the PDB website.
> This creates a .cif file but removes SS info.
> Your way of doing things creates .cif files with SS info in them (at
> least in my hands phenix works better here). The fact that Chimera
> does not read SS info from cif files is another story, but cif support
> is limited.
> I think this is as good as it gets. Most importantly, my pdbs are in
> order, so I should now be in the clear - regardless what individual
> viewers display. Thank you for the explanation!
> Maciej
>
> On Thu, Jun 28, 2018 at 4:37 PM, Oleg Sobolev <osobolev at lbl.gov
> <mailto:osobolev at lbl.gov>> wrote:
>
> Hi Maciej,
>
> 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)
>
> Can you describe more specifically what exactly the tool you are
> using? One way around it would be to convert your pdb to mmcif using
> phenix.pdb_as_cif
> tool which will preserve SS information.
>
> How can you have SS elements displayed if it description is
> missing from the header?
>
> As pointed by Ricardo, visualization programs usually can display
> SS without any header. On top of that, whether they will use the
> header if it is present - also depend on particular program.
>
> Best regards,
> Oleg Sobolev.
>
> 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
> <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
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
> http://phenix-online.org/mailman/listinfo/phenixbb
> <http://phenix-online.org/mailman/listinfo/phenixbb>
> Unsubscribe: phenixbb-leave at phenix-online.org
> <mailto: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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20180629/39b95497/attachment-0001.htm>
More information about the phenixbb
mailing list