Re: [ccp4bb] Refinement with twinned data question
1-So for my case, I should try and generate Rfree flags, in the higher apparent C 2 2 21 and not the real P 1 21 1, correct? 2-I noticed that if I used the output PHIC FOM data, the maps looked awesome! Too good almost... Thanks a lot On Sun, 2 Oct 2011 12:07:22 +0100, Garib N Murshudov wrote: > Dear Yuri > 1) For twin refinement refmac internally changes free reflections so that twin related reflections belong to the same class (twin or working). However it would be good to generate free reflections in higher space group that would include twin and space group symmetries. > 2) You should always use original data for refinement. Never use output from refmac for next round of refinement. Output mtz file is representation of model. > regards > Garib > > On 2 Oct 2011, at 03:27, Yuri wrote: > >> Dear all, >> I have some questions about the correct protocol for refinement of twinned data (0.46) >> >> 1- How do I ensure that my Rfree set is generated properly? >> >> 2-I noticed that if I enable intensity based twin refinement, refmac estimates the correct twin fraction >> law -h,-k,h+l. But for subsequent refinement rounds should I keep using the raw intensity mtz file or >> the newly generated mtz with PHIC and FOM information? >> >> Thank you >> -- >> Yuri Pompeu > > Garib N Murshudov > Structural Studies Division > MRC Laboratory of Molecular Biology > Hills Road > Cambridge > CB2 0QH UK > Email: ga...@mrc-lmb.cam.ac.uk [1] > Web http://www.mrc-lmb.cam.ac.uk [2] -- Yuri Pompeu Links: -- [1] mailto:jen...@mrc-lmb.cam.ac.uk [2] http://www.mrc-lmb.cam.ac.uk/
Re: [ccp4bb] Refinement with twinned data question
Dear Yuri 1) For twin refinement refmac internally changes free reflections so that twin related reflections belong to the same class (twin or working). However it would be good to generate free reflections in higher space group that would include twin and space group symmetries. 2) You should always use original data for refinement. Never use output from refmac for next round of refinement. Output mtz file is representation of model. regards Garib On 2 Oct 2011, at 03:27, Yuri wrote: > Dear all, > I have some questions about the correct protocol for refinement of twinned > data (0.46) > > 1- How do I ensure that my Rfree set is generated properly? > > 2-I noticed that if I enable intensity based twin refinement, refmac > estimates the correct twin fraction > law -h,-k,h+l. But for subsequent refinement rounds should I keep using the > raw intensity mtz file or > the newly generated mtz with PHIC and FOM information? > > Thank you > -- > Yuri Pompeu Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
[ccp4bb] Refinement with twinned data question
Dear all, I have some questions about the correct protocol for refinement of twinned data (0.46) 1- How do I ensure that my Rfree set is generated properly? 2-I noticed that if I enable intensity based twin refinement, refmac estimates the correct twin fraction law -h,-k,h+l. But for subsequent refinement rounds should I keep using the raw intensity mtz file or the newly generated mtz with PHIC and FOM information? Thank you -- Yuri Pompeu
