[phenixbb] Incorrect secondary structure assignment in a .pdb

Maciej Jagielnicki mjj5qk at virginia.edu
Thu Jun 28 09:23:00 PDT 2018

 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...

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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