[phenixbb] fix part of structure during refinement

Jorge Iulek iulek at uepg.br
Sun Apr 6 16:47:40 PDT 2014

Dear all,

     I want to test a refinement in which I fix part of my structure 
(say, residues 1 to 244 in chains C and D, and chains A and B 
completely) while the rest is to be refined with annealing.
     From the manual and 
http://www.phenix-online.org/pipermail/phenixbb/2009-June/013358.html, I 
have in my parameter file:

  refine {
     strategy = *individual_sites individual_sites_real_space rigid_body \
                individual_adp group_adp tls *occupancies group_anomalous
     sites {
       individual = ( chain C and resseq 245:259 ) or ( chain D and 
resseq 245:259 )
       torsion_angles = None
       rigid_body = None

     I thought atoms out of the selection in the output structure 
(chains A and B + residues 1 to 244 in chains C and D) would keep the 
same coordinates as they were input. But I see all structure atoms 
changed coordinates. I also tried to turn off tls and ncs usage, but the 
picture is the same.
     What do I miss here, to be able to fix some atoms during refinement?


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