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

[Pavel Afonine]

Hi Maxime,

no, the next one should have it.

Pavel

On 1/16/13 7:22 AM, Maxime Cuypers wrote:
> 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
>>
>