<div dir="ltr">Yea,<div>That was dumb. Sorry. Vinyl is a double bond. Sleepy time for me.</div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Jun 19, 2014 at 1:32 PM, Edward A. Berry <span dir="ltr"><<a href="mailto:BerryE@upstate.edu" target="_blank">BerryE@upstate.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">No, those are actually double bonds (hence the name "vinyl"),<br>
unless it it is a c-type heme, in which case you should be using HEC.cif<br>
$CCP4/lib/data/monomers/h/HEM.<u></u>cif:<br>
HEM CBC CAC double 1.329 0.020<br>
HEM CBB CAB double 1.330 0.020<br>
$CCP4/lib/data/monomers/h/HEC.<u></u>cif<br>
HEC CBC CAC single 1.510 0.020<br>
HEC CBB CAB single 1.510 0.020 <br>
This is because cysteine Sg's covalently link the vinyl groups,<br>
adding across the double bond as it were.<br>
Unless you have trypanosome or Euglena cytochrome,<br>
in which case one vinyl is native and the other<br>
is substituted by cysteine.<br>
eab<div><div class="h5"><br>
<br>
On 06/19/2014 03:11 PM, Yarrow Madrona wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
Hello,<br>
<br>
The HEM.cif in $Phenix/chem_data/mon_lib<br>
has ideal angles of 1.337 for single bonds on the vinyl groups.<br>
<br>
HEM CAC CBC coval 1.337 0.02<br>
<br>
HEM CAB CBB coval 1.337 0.02<br>
<br>
As far as I know these are single bonds and the ideal bond angles should be around 1.5.<br>
<br>
-Yarrow<br>
<br>
<br></div></div>
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</blockquote>
</blockquote></div><br></div>