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

[Pavel Afonine]

Hi Maxime,

this problem is now addressed in phenix.refine and other related tools 
(such as phenix.pdbtools, phenix.model_vs_data, 
phenix.geometry_minimization): next available nightly build should have 
it. The correct distances are used based on "scattering_table=neutron" 
flag in phenix.refine and phenix.model_vs_data, and 
"use_neutron_distances=true" in phenix.pdbtools and 
phenix.geometry_minimization.

Please let me know should you have any questions and notice any problems.

Thanks,
Pavel


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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