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

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