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It is a bug. Thanks for letting us know!<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/28/18 13:43, Ricardo Righetto
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAB7-RrsqG5BY8-usQECTPwZQs_ZeRwq5ucgaapFACtavfhz1vg@mail.gmail.com">
<div dir="ltr">
<div>Dear Pavel,</div>
<div><br>
</div>
<div>An example of Phenix tool that does not preserve
HELIX/SHEET records is phenix.ready_set (I have version
1.13-2998). Is this a bug or normal behavior? (apologies for
getting slightly off topic)<br>
</div>
<div><br>
</div>
<div>And thanks for clarifying about the behavior of secondary
structure restraints in phenix.real_space_refine!</div>
<div><br>
</div>
<div>Best wishes,<br>
</div>
<div><br>
</div>
<div><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 22:26 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 clarification Ricardo and Pavel.</div>
<div><br>
</div>
<div>It still amazes me though that different pdb viewers
would make such ridiculous SS predictions/assignments at
times for a file that does not come with that
information in the header. <br>
</div>
<div>And it seems that during a deposition to PDB I have
to manually add the location of helices/sheets into the
.cif files generated by the deposition
system...otherwise I go for deposition somewhat blind
(this has of course nothing to do with Phenix, but adds
more to my confusion).<span class="HOEnZb"><font
color="#888888"><br>
</font></span></div>
<span class="HOEnZb"><font color="#888888">
<div><br>
</div>
<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 4:16
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"> 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_res<wbr>traints
(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.<span
class="m_-3494054036116591019HOEnZb"><font
color="#888888"><br>
<br>
Pavel</font></span>
<div>
<div class="m_-3494054036116591019h5"><br>
<br>
<div
class="m_-3494054036116591019m_-5665897240554644927moz-cite-prefix">On
6/28/18 13:10, Ricardo Righetto wrote:<br>
</div>
<blockquote type="cite">
<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"
target="_blank"
moz-do-not-send="true">https://plato.cgl.ucsf.edu/chi<wbr>mera/docs/UsersGuide/midas/ksd<wbr>ssp.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="m_-3494054036116591019m_-5665897240554644927gmail_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="m_-3494054036116591019m_-5665897240554644927HOEnZb"><font
color="#888888">
<div>Maciej<br>
</div>
</font></span></div>
<div
class="m_-3494054036116591019m_-5665897240554644927HOEnZb">
<div
class="m_-3494054036116591019m_-5665897240554644927h5">
<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_-3494054036116591019m_-5665897240554644927m_-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_-3494054036116591019m_-5665897240554644927m_-5063945019541963886HOEnZb"><font
color="#888888"><br>
Pavel</font></span>
<div>
<div
class="m_-3494054036116591019m_-5665897240554644927m_-5063945019541963886h5"><br>
<br>
<br>
<div
class="m_-3494054036116591019m_-5665897240554644927m_-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>
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of Virginia <br>
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Physiology and
Biological
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style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">480
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