[phenixbb] how to modify C-D bond length restraints in phenix?
maximecuypers at gmail.com
Tue Nov 6 09:45:30 PST 2012
i am refining a perdeuterated neutron structure and have noticed a lot of
positive density aside the D atoms on aliphatic and aromatic side chains.
just in the alignment of C-D bonds (C-D then +), suggesting that
phenix.refine constraints these bond lengths too short in my case. i tried
automatic weights for geometry refinement and unrestrained specific C-D
refinement but it is not satisfactory.
then i found the following funny distances (angströms) in the pdb database
C-D aromatics = 0.93-0.94
C-D aliph. = 0.98
Program : xplor3.1
D-protein (despite the atoms being labelled as H according to abstract)
C-D aromatics = 1.06-1.08
C-D aliph. = 1.08
C-H aromatics = 0.93
C-H aliph. = 0.97
C-H aromatics = 1.06-1.10
C-H aliph. = 1.09
those neutron C-D/C-H bond lengths in pdb seem pretty much inconsistentto
So it seems that phenix.refine uses C-D/ C-H bonds restrains that are
different to other programs to below 1.0 Ang. ( ca. 0.10 A differences)
how can i change the restraints to make it all longer bond lengths for C-D
only? with a .cif file?
i saw that phenix uses the CCP4 monomer library but the one in :
only seem to be applying modifications.
any clue on how to specifically modify the restraints parameters on C-D
bonds would be very appreciated.
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