[phenixbb] how to modify C-D bond length restraints in phenix?

Pavel Afonine pafonine at lbl.gov
Tue Nov 6 10:14:20 PST 2012

Hi Maxime,

it's not you doing anything wrong.

phenix.refine uses X-ray distances for target -H bond lengths, which are 
shorter than neutron ones. Sorry.

We are working on resolving this problem.

I can think of only one quick fix that would allow you to keep going 
(and not wait until we come up with the solution). This is bad and 
awful, but here it is:

In your Phenix copy manually change -H bond length definitions for all 
amino acid cif files found here "../chem_data/geostd" so they correspond 
to neutron distances. If you have non-amino acid residues then you will 
need to change their cifs in "../chem_data/mon_lib" as well.

Any better solutions are welcome of course.


On 11/6/12 9:45 AM, Maxime Cuypers wrote:
> Hi,
> 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 neutron structures:
> 3KYX:
> program: Phenix.refine
> D-prot
> Distances:
> C-D aromatics = 0.93-0.94
> C-D aliph. =  0.98
> 1CQ2
> Program : xplor3.1
> D-protein (despite the atoms being labelled as H according to abstract)
> Distances:
> C-D aromatics = 1.06-1.08
> C-D aliph. = 1.08
> 4FC1
> H-protein
> Distances:
> program: Phenix.refine
> C-H aromatics = 0.93
> C-H aliph. = 0.97
> 1VCX
> H-protein
> program: CNS
> Distances:
> 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 me.
> 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 :
> /usr/local/phenix-.../chem_data/mon_lib/list
> only seem to be applying modifications.
> any clue on how to specifically modify the restraints parameters on 
> C-D bonds would be very appreciated.
> Thanks,
> Maxime

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