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The point is that no automated secondary structure (SS) annotation
software can assign SS fully correctly simply because it relies on
input model geometry, and models that are subject to refinement are
rarely perfect for these software to do a great job. This is why the
Manual (see previous email) recommends getting initial automated
assignment first using phenix.secondary_structure_restraints (which
uses various annotation methods, including ksdssp) and then manually
checking and editing it if necessary.<br>
<br>
Tools within Phenix always preserve HELIX/SHEET records in PDB
files. Let us know if you have an example where this is not the
case.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/28/18 13:10, Ricardo Righetto
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAB7-Rrupy4hibxA35GsfO3qAx9On4k1+XyRT3_uFQU59a4=wnA@mail.gmail.com">
<div dir="ltr">
<div>Hi Maciej,</div>
<div><br>
</div>
<div>If the PDB file has no secondary structure assignments
defined in the header and you open it in Chimera, it
automatically runs ksdssp in the background to assign helices
and sheets, which may or may not be correct and might make you
think that you have secondary structure records in the header
when you actually have nothing:</div>
<div><a
href="https://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html"
moz-do-not-send="true">https://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html</a></div>
<div><br>
</div>
<div>If in turn you save the PDB from Chimera with such
automatically generated assignments, the records corresponding
to this assignment will be written to the header. And if it's
written in the header, by default phenix.real_space_refine
will use these restraints.<br>
</div>
<div><br>
</div>
<div>Bottom line is that throughout modelling and refinement you
should always inspect your output PDB file from whatever
program you use (PHENIX, Coot, Chimera, etc) to make sure that
the information you think should be in the header is indeed
there. I agree that some programs might unnecessarily "get
rid" of the secondary structure records in the header and this
is a bit annoying.</div>
<div><br>
</div>
<div>Hope this helps,<br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div class="gmail_signature" data-smartmail="gmail_signature"><br>
--<br>
Ricardo Diogo Righetto<br>
</div>
</div>
<br>
<div class="gmail_quote">2018-06-28 20:02 GMT+02:00 Maciej
Jagielnicki <span dir="ltr"><<a
href="mailto:mjj5qk@virginia.edu" target="_blank"
moz-do-not-send="true">mjj5qk@virginia.edu</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>Thank you for the suggestion. <br>
</div>
<div><br>
</div>
<div>Nothing changes when I run phenix real space
refinement with SS restraints turned on. I can either
input a .pdb file with correct SS information in the
header or a .pdb file with no SS information at all and
the end result (new refined .pdb) is the same file with
the same SS information in a new header. The information
stays the same and 'correct'.<br>
</div>
<div><br>
</div>
<div>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) remove the header SS
information altogether (why you would do that for PDB
deposition is unknown to me), that resulting .pdb file
still shows SS elements in different pdb viewers but SS
info is no longer correct. How can you have SS elements
displayed if it description is missing from the header?
<br>
</div>
<span class="HOEnZb"><font color="#888888">
<div>Maciej<br>
</div>
</font></span></div>
<div class="HOEnZb">
<div class="h5">
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Jun 28, 2018 at 12:38
PM, Pavel Afonine <span dir="ltr"><<a
href="mailto:pafonine@lbl.gov" target="_blank"
moz-do-not-send="true">pafonine@lbl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> Hi Maciej,<br>
<br>
please have a look at item #10 and Notes section
here:<br>
<br>
<a
class="m_-5063945019541963886m_-3497824760541395042moz-txt-link-freetext"
href="http://www.phenix-online.org/documentation/reference/real_space_refine.html"
target="_blank" moz-do-not-send="true">http://www.phenix-online.org/d<wbr>ocumentation/reference/real_sp<wbr>ace_refine.html</a><br>
<br>
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.<br>
<br>
If you have more questions please get back to
us!<br>
<br>
Good luck!<span
class="m_-5063945019541963886HOEnZb"><font
color="#888888"><br>
Pavel</font></span>
<div>
<div class="m_-5063945019541963886h5"><br>
<br>
<br>
<div
class="m_-5063945019541963886m_-3497824760541395042moz-cite-prefix">On
6/28/18 09:23, Maciej Jagielnicki wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<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="m_-5063945019541963886m_-3497824760541395042gmail_signature"
data-smartmail="gmail_signature">
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<div>Maciej
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<div class="m_-5063945019541963886gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">
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<div dir="ltr">
<div>
<div dir="ltr">
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<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>
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<div><font face="arial,
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434-243-2520</font></div>
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