Re: [phenixbb] Incorrect secondary structure assignment in a .pdb

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 mailto:[email protected]> 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 mailto:[email protected]> 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

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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