<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&#39;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 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 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 href="mailto:gregc@cgl.ucsf.edu" target="_blank">gregc@cgl.ucsf.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
  
    
  
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    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 &quot; mmCIF does not support references to
    save frames or the use of save frames for purposes other than for
    encapsulating dictionary definitions&quot;
    [<a href="http://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html" target="_blank">http://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html</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&#39;s are &quot;fixed&quot;, 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 href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511" 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" target="_blank"></a><a href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511" target="_blank">https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511</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 href="http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_sites_footnote.html" target="_blank">http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_sites_footnote.html</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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