<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">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">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">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">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">
<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><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
</div></div></div>
</blockquote></div><br><br clear="all"><br>-- <br><div class="m_-5063945019541963886gmail_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>
</div>
</div></div><br>______________________________<wbr>_________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/<wbr>mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.<wbr>org</a><br></blockquote></div><br></div>