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<div>Hi All,</div><div><br></div><div>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.<br></div><div><br></div><div>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... </div>
<br clear="all"><div>Regards,</div><div>Maciej J.<br></div><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>Maciej Jagielnicki, MS.<div>Graduate Student</div><div><span style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">University of Virginia <br></span></div><div><span style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">Molecular Physiology and Biological Physics<br></span></div><div><span style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">480 Ray C Hunt Drive Rm 320<br></span></div><div><span style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">Charlottesville, VA<br></span></div><div><font face="arial, sans-serif">Lab Phone: 434-243-2520</font></div><div><font face="arial, sans-serif"><br></font></div></div></div></div></div></div></div></div></div></div></div></div>
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