<div dir="ltr">I wouldn&#39;t necessarily say they are ridiculous. If you choose to show a cartoon, some viewers run in the background a secondary structure analysis program (dssp and variants thereof) and depending on the threshold will assign automatically secondary structure elements. None of these automatic routines is perfect and even if you do it manually, opinions between different people will give a spread in terms of when to draw a helix or how long it should be for example. However, no one has to use the provided ss definitions in a file. If someone downloads a file from the pdb and interprets the structrue might disagree with the boundaries and definitions of the secondary structure provided and amend them.¬†¬†<div><br></div><div>Cheers</div><div>Christian¬†</div></div><br><div class="gmail_quote"><div dir="ltr">On Thu, Jun 28, 2018 at 9:27 PM Maciej Jagielnicki &lt;<a href="mailto:mjj5qk@virginia.edu">mjj5qk@virginia.edu</a>&gt; wrote:<br></div><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).<br></div><div><br></div><div>Maciej <br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jun 28, 2018 at 4:16 PM, Pavel Afonine <span dir="ltr">&lt;<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>&gt;</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_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.<span class="m_3580634942624476438HOEnZb"><font color="#888888"><br>
    <br>
    Pavel</font></span><div><div class="m_3580634942624476438h5"><br>
    <br>
    <div class="m_3580634942624476438m_-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">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&#39;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 &quot;get
          rid&quot; 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_3580634942624476438m_-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">&lt;<a href="mailto:mjj5qk@virginia.edu" target="_blank">mjj5qk@virginia.edu</a>&gt;</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 &#39;correct&#39;.<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_3580634942624476438m_-5665897240554644927HOEnZb"><font color="#888888">
                  <div>Maciej<br>
                  </div>
                </font></span></div>
            <div class="m_3580634942624476438m_-5665897240554644927HOEnZb">
              <div class="m_3580634942624476438m_-5665897240554644927h5">
                <div class="gmail_extra"><br>
                  <div class="gmail_quote">On Thu, Jun 28, 2018 at 12:38
                    PM, Pavel Afonine <span dir="ltr">&lt;<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>&gt;</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_3580634942624476438m_-5665897240554644927m_-5063945019541963886m_-3497824760541395042moz-txt-link-freetext" href="http://www.phenix-online.org/documentation/reference/real_space_refine.html" target="_blank">http://www.phenix-online.org/documentation/reference/real_space_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_3580634942624476438m_-5665897240554644927m_-5063945019541963886HOEnZb"><font color="#888888"><br>
                            Pavel</font></span>
                        <div>
                          <div class="m_3580634942624476438m_-5665897240554644927m_-5063945019541963886h5"><br>
                            <br>
                            <br>
                            <div class="m_3580634942624476438m_-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>
                                -- <br>
                                <div class="m_3580634942624476438m_-5665897240554644927m_-5063945019541963886m_-3497824760541395042gmail_signature" data-smartmail="gmail_signature">
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                                            <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>
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                                                      <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>
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                                </div>
                              </div>
                            </blockquote>
                            <br>
                          </div>
                        </div>
                      </div>
                    </blockquote>
                  </div>
                  <br>
                  <br clear="all">
                  <br>
                  -- <br>
                  <div class="m_3580634942624476438m_-5665897240554644927m_-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>
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        <br>
      </div>
    </blockquote>
    <br>
  </div></div></div>

</blockquote></div><br><br clear="all"><br>-- <br><div class="m_3580634942624476438gmail_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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