this doesnt exactly go to the detail i was looking for...
but thanks, i do know where the pages are.
tommi
On Nov 26, 2009, at 9:52 PM, Jacques-Philippe Colletier wrote:
> Hi Tommi
>
> You will find all the information you need on the following web page:
>
> http://www.phenix-online.org/documentation/refinement.htm
>
> as per your question, you could try :
>
> phenix.refine yourdataset.mtz yourmodel.pdb strategy=rigid_body
> rigid_body.number_of_zones=1 sites.rigid_body="chain A"
> sites.rigid_body="chain B" sites.rigid_body="chain C"
> sites.rigid_body="chain D" etc...
>
> (I suggest you take only one zone for the rigid body refinement
> because at 6A you only have so many reflections)
>
> Best
> Jacques
>
> Le Nov 26, 2009 à 8:32 PM, Tommi Kajander a écrit :
>
>> Apologies, i know this is not phenix bb but since i am here (and
>> not subscr. there), does anyone
>> know how to control rigid body ref positions in phenix.refine, i am
>> trying to do very low res check
>> (6 Å) with quite many molecules, and they start landing on each
>> other while the MR solution from molrep
>> has perfect packing ....isnt there a packing constraint somwhere
>> saying atoms cant be on top of each
>> other...???? there was something about clashes but didnt seem to do
>> anything.. the parameter definitions
>> in .eff are bit cryptic to me in places...
>>
>> (would it be possible to step back a bit (sorry if i am wrong) to
>> the ancient world of x-plor,
>> still like that manual a lot..).
>>
>> thanks
>> Tommi K.
>
>
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p. +358-9-19158903
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