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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"><<a moz-do-not-send="true"
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 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"><<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>></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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<br>
<br>
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