<div dir="ltr">Hi Maciej,<div><br></div><div>I would add that you can obtain recreated SS annotations for your model using</div><div>phenix.secondary_structure_restraints &lt;your model&gt;¬†ignore_annotation_in_file=True¬†format=pdb</div><div><br></div><div>More on this:</div><div><a href="https://www.phenix-online.org/documentation/reference/secondary_structure_restraints.html">https://www.phenix-online.org/documentation/reference/secondary_structure_restraints.html</a><br></div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jun 28, 2018 at 9:38 AM, 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_-6918196201767132165moz-txt-link-freetext" href="http://www.phenix-online.org/documentation/reference/real_space_refine.html" target="_blank">http://www.phenix-online.org/<wbr>documentation/reference/real_<wbr>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="HOEnZb"><font color="#888888"><br>
    Pavel</font></span><div><div class="h5"><br>
    <br>
    <br>
    <div class="m_-6918196201767132165moz-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_-6918196201767132165gmail_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>

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