No, those are actually double bonds (hence the name "vinyl"), unless it it is a c-type heme, in which case you should be using HEC.cif $CCP4/lib/data/monomers/h/HEM.cif: HEM CBC CAC double 1.329 0.020 HEM CBB CAB double 1.330 0.020 $CCP4/lib/data/monomers/h/HEC.cif HEC CBC CAC single 1.510 0.020 HEC CBB CAB single 1.510 0.020 This is because cysteine Sg's covalently link the vinyl groups, adding across the double bond as it were. Unless you have trypanosome or Euglena cytochrome, in which case one vinyl is native and the other is substituted by cysteine. eab On 06/19/2014 03:11 PM, Yarrow Madrona wrote:
Hello,
The HEM.cif in $Phenix/chem_data/mon_lib has ideal angles of 1.337 for single bonds on the vinyl groups.
HEM CAC CBC coval 1.337 0.02
HEM CAB CBB coval 1.337 0.02
As far as I know these are single bonds and the ideal bond angles should be around 1.5.
-Yarrow
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