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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 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>].
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<br>
<br>
<div class="moz-cite-prefix">On 11/11/2015 10:11 AM, Oliver Clarke
wrote:<br>
</div>
<blockquote
cite="mid:AAA68F75-0DEE-4F08-925B-99ABE39249CB@gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Hi all,<br class="">
<div>
<div class=""><br style="font-family: Helvetica; font-size:
12px; font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align:
start; text-indent: 0px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align:
start; text-indent: 0px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; float: none; display: inline
!important;" class="">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"
style="font-family: Helvetica; font-size: 12px; font-style:
normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width:
0px;" class=""><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; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width:
0px; float: none; display: inline !important;" class="">),
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"
class="">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; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width:
0px;" class="">
<br style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align:
start; text-indent: 0px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align:
start; text-indent: 0px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; float: none; display: inline
!important;" class="">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; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width:
0px;" class="">
<br style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align:
start; text-indent: 0px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align:
start; text-indent: 0px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; float: none; display: inline
!important;" class="">Cheers,</span><br style="font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; orphans: auto; text-align:
start; text-indent: 0px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; float: none; display: inline
!important;" class="">Oliver.</span></div>
</div>
<br class="">
<br>
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<br>
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