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

[Maxime Cuypers]

Hi Pavel,

Many thanks for this,
i guess this is not yet in the version from the 14th ?

cheers
Maxime

2013/1/14, Pavel Afonine <pafonine at lbl.gov>:
> 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
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
>


-- 
Dr. Maxime Cuypers
Institut Laue Langevin (ILL), Deuteration lab
Rue Jules Horowitz, 6, BP 156
38042 Grenoble cedex 9
France
Tel +33 (0)4 76 20 94 74
Fax +33 (0)4 76 20 71 20
http:\\www.ill.fr\deuteration