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
tommi.kajan...@helsinki.fi
