<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"><<a href="mailto:olibclarke@gmail.com" target="_blank">olibclarke@gmail.com</a>></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"><<a href="mailto:gregc@cgl.ucsf.edu" target="_blank">gregc@cgl.ucsf.edu</a>></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 " mmCIF does not support references to
save frames or the use of save frames for purposes other than for
encapsulating dictionary definitions"
[<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'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 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>
</div>
<br>
<br>
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