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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.<br>
<br>
A tool that may be handy in this context is
phenix.secondary_structure_validation which validates SS records.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/29/18 08:05, Maciej Jagielnicki
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAHLTAE+suwMGFCd=FhhYECcaR26=KiLgoH=-zn6h=6hOYxBKPg@mail.gmail.com">
<div dir="ltr">
<div>Thanks Oleg,</div>
<div>I was using the 'pdb extract' online tool provided by the
PDB website. This creates a .cif file but removes SS info.</div>
<div>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.</div>
<div>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!</div>
<div>Maciej<br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Jun 28, 2018 at 4:37 PM, Oleg
Sobolev <span dir="ltr"><<a href="mailto:osobolev@lbl.gov"
target="_blank" moz-do-not-send="true">osobolev@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 dir="ltr">Hi Maciej,
<div class="gmail_extra"><br>
<div class="gmail_quote"><span class="">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<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) </div>
</div>
</blockquote>
</span>
<div>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 </div>
<div>phenix.pdb_as_cif</div>
<div>tool which will preserve SS information.</div>
<span class="">
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div> How can you have SS elements displayed if
it description is missing from the header? <br>
</div>
</div>
</blockquote>
</span>
<div>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.</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Oleg Sobolev.</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div class="h5">
<div class="m_2921074794165246987HOEnZb">
<div class="m_2921074794165246987h5">
<div class="gmail_extra">
<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_2921074794165246987m_-4408072773680048743m_-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_2921074794165246987m_-4408072773680048743HOEnZb"><font
color="#888888"><br>
Pavel</font></span>
<div>
<div
class="m_2921074794165246987m_-4408072773680048743h5"><br>
<br>
<br>
<div
class="m_2921074794165246987m_-4408072773680048743m_-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>
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