[phenixbb] Group ADP not working

alebus at pasteur.edu.uy alebus at pasteur.edu.uy
Tue Jun 3 07:16:45 PDT 2008

Dear all,

I am refining a structure (2.9angs res; P21) with phenix (Version:  
1.3b; Release tag: rc6; linux platform)

I want to carry on group_ADP refinement, according to the ('lengthy')  
command line :

phenix.refine eden_unique1.hkl hlcoeff_blur.hkl abril28_phenix.pdb  
input.experimental_phases.labels="PA_BLUR PB_BLUR PC_BLUR PD_BLUR"  
ordered_solvent=false simulated_annealing=false  
strategy=rigid_body+individual_sites+group_adp+tls main.ncs=tru
e main.number_of_macro_cycles=10 xray_data.low_resolution=15.0  
xray_data.high_resolution=2.7 tls_group_selections.params  
rigid_body_selections.params group_anomalous_1.params  
elbow.acp_A_pdb.001.cif restraints_edits.params  

everything works just fine (including correct handling of an 'unusual'  
ligand; selected NCS restraints; TLS; etc)...except for the group ADP  
: phenix keeps doing individual atom B-factor refinement

(e.g. these are some pertinent remarks in the output pdb

REMARK leading digit, like 1_, means number of macro-cycle
REMARK 0    : statistics at the very beginning when nothing is done yet
REMARK 1_bss: bulk solvent correction and/or (anisotropic) scaling
REMARK 1_xyz: refinement of coordinates
REMARK 1_rbr: rigid body refinement
REMARK 1_gbr: group B-factor refinement
REMARK  R-factors, x-ray target values and norm of gradient of x-ray target
REMARK  stage     r-work r-free  xray_target_w  xray_target_t
REMARK    0    :  0.3951 0.4346  -6.345353e+00  -6.295977e+00
REMARK    1_bss:  0.3189 0.3519  -6.182904e+00  -6.132416e+00
REMARK    1_rbr:  0.3199 0.3553  -6.164872e+00  -6.111524e+00
REMARK    1_bss:  0.3197 0.3548  -6.158236e+00  -6.106543e+00
REMARK    1_xyz:  0.3145 0.3612  -6.243414e+00  -6.163029e+00
REMARK    1_adp:  0.2890 0.3327  -6.111496e+00  -6.011406e+00
REMARK    2_bss:  0.2862 0.3290  -6.107396e+00  -6.004629e+00
REMARK    2_xyz:  0.2801 0.3278  -6.104559e+00  -5.995221e+00
REMARK    2_adp:  0.2783 0.3213  -6.062947e+00  -5.954846e+00
REMARK    3_bss:  0.2783 0.3214  -6.063301e+00  -5.955103e+00
REMARK    3_xyz:  0.2755 0.3218  -6.065099e+00  -5.950739e+00
REMARK    3_adp:  0.2751 0.3218  -6.062715e+00  -5.947567e+00
and so on, always doing 'X_adp' (and not 'X_gbr') on the different steps...

starting from a single value on the B-factor column in the input pdb,  
of course I end up having individually varied figures in the end,  
which I don't want

I will greatly appreciate any help on what am I doing wrong.



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