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    Noted.  I've added this to the list of things to do for ChimeraX
    (formerly known as Chimera2).<br>
    <br>
      -- Greg<br>
    <br>
    <div class="moz-cite-prefix">On 11/12/2015 02:21 PM, Oliver Clarke
      wrote:<br>
    </div>
    <blockquote
cite="mid:CAPghYOp0OnLWJ=grqVtdnSuCt3vOv3HpXutRo083aO5KhR8b0g@mail.gmail.com"
      type="cite">
      <div dir="ltr">
        <div>Relating to this, I wonder whether it is possible to find a
          home for attributes calculated in Chimera 2 in one of the
          mmCIF fields? <br>
          <br>
          I mean that's the advantage of mmCIF in theory right, that it
          is extensible and can support attributes beyond just position
          and B-factor?<br>
          <br>
          This would make transferring custom defined or calculated
          attributes between different chimera sessions much easier I
          think, if they were inherent to the file containing the
          coordinates, and again would at least allow for the
          possibility of data exchange with other programs.<br>
          <br>
        </div>
        Oliver.<br>
      </div>
      <div class="gmail_extra"><br>
        <div class="gmail_quote">On Thu, Nov 12, 2015 at 4:49 PM, Oliver
          Clarke <span dir="ltr">&lt;<a moz-do-not-send="true"
              href="mailto:olibclarke@gmail.com" target="_blank">olibclarke@gmail.com</a>&gt;</span>
          wrote:<br>
          <blockquote class="gmail_quote" style="margin:0 0 0
            .8ex;border-left:1px #ccc solid;padding-left:1ex">
            <div dir="ltr">
              <div>
                <div>I see what you mean Greg... it is not at all clear
                  how to use this now that I look at it in more detail.
                  <br>
                  <br>
                  A hack using this entry as a handle for persistent
                  notes would certainly be useful in the medium term,
                  but in the longer term it would be nice to have a
                  established syntax, so that notes written in Chimera
                  could be read and displayed in Coot, for example (see
                  here for discussion: <a moz-do-not-send="true"
                    href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=coot;8213db52.1511"
                    target="_blank">https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=coot;8213db52.1511</a>).
                  <br>
                  <br>
                  But I guess this might require some discussion with
                  the PDB - according to their FAQ old-school PDB files
                  will become obsolete next year and mmCIF/PDBx will be
                  the only game in town...<br>
                  <br>
                </div>
                Cheers,<br>
              </div>
              Oliver.<br>
            </div>
            <div class="HOEnZb">
              <div class="h5">
                <div class="gmail_extra"><br>
                  <div class="gmail_quote">On Thu, Nov 12, 2015 at 4:22
                    PM, Greg Couch <span dir="ltr">&lt;<a
                        moz-do-not-send="true"
                        href="mailto:gregc@cgl.ucsf.edu" target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:gregc@cgl.ucsf.edu">gregc@cgl.ucsf.edu</a></a>&gt;</span>
                    wrote:<br>
                    <blockquote class="gmail_quote" style="margin:0 0 0
                      .8ex;border-left:1px #ccc solid;padding-left:1ex">
                      <div bgcolor="#FFFFFF" text="#000000"> That is an
                        excellent suggestion.  Currently the mmCIF files
                        from the PDB provide the free-form text for the
                        footnote, but do not provide the data that is
                        supposed to be in the associated
                        conformer_family_coord_set category.  And
                        without that data, it will be difficult to
                        figure out and show exactly which atoms/residues
                        are associated with the footnote.  It looks like
                        that part of the mmCIF specification is unused
                        because it is not well thought out.  The
                        conformer_family_coord_set data category makes
                        references to CIF save frames, but currently "
                        mmCIF does not support references to save frames
                        or the use of save frames for purposes other
                        than for encapsulating dictionary definitions" [<a
                          moz-do-not-send="true"
href="http://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html"
                          target="_blank"><a class="moz-txt-link-freetext" href="http://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html">http://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html</a></a>]. 

                        And since there are no examples, so it is
                        unclear how the mmCIF committee was expecting
                        this to work.<br>
                        <br>
                        So until atom_sites_footnote's are "fixed", is
                        getting access to the text okay?  We could
                        probably extract the relevant residues from the
                        free-form text most of the time, but it would be
                        a hack.<br>
                        <br>
                           -- Greg
                        <div>
                          <div><br>
                            <br>
                            <div>On 11/11/2015 10:11 AM, Oliver Clarke
                              wrote:<br>
                            </div>
                          </div>
                        </div>
                        <blockquote type="cite">
                          <div>
                            <div> Hi all,<br>
                              <div>
                                <div><br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
                                  <span
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">As
                                    discussed on the ccp4bb (</span><a
                                    moz-do-not-send="true"
href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511"
                                    target="_blank"><a class="moz-txt-link-freetext" href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511">https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511</a></a><span
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">),

                                    the mmCIF format incorporates an
                                    atom_sites_foornote record (<a
                                      moz-do-not-send="true"
href="http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_sites_footnote.html"
                                      target="_blank"><a class="moz-txt-link-freetext" href="http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_sites_footnote.html">http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_sites_footnote.html</a></a>)
                                    which allows for the direct
                                    association of specific
                                    comments/annotations with particular
                                    atoms/residues.</span><br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
                                  <br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
                                  <span
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">As
                                    part of expanding mmCIF support in
                                    Chimera2, would it be possible to
                                    consider incorporating the capacity
                                    to read, write, and display these
                                    records as labels or notes? This
                                    could be a great way of
                                    incorporating built-in-annotations
                                    in a structure pertaining to
                                    specific features that could
                                    potentially be readable by other
                                    software such as Coot and pymol.</span><br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
                                  <br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
                                  <span
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Cheers,</span><br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
                                  <span
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Oliver.</span></div>
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</pre>
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