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 simulated_annealing.mode=first 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 convert_to_isotropic=true 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 ****************** REFINEMENT STATISTICS STEP BY STEP ****************** 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 ------------------------------------------------------------------------ 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. Thanks, Alejandro
Hi Alejandro, 1) it does group isotropic B refinement but it's hidden as inside step of TLS refinement, so you don't see it as a separate step. 2) You get different B-factors because you do TLS refinement. Look at TLS formula and you will see that each individual atoms is supposed to get different anisotropic B. Nothing wrong about it. Please let me know if you have any other questions or problems or my explanations were not clear! BTW, you can use parameter files instead of typing such a long command line. Pavel. On 6/3/2008 7:16 AM, [email protected] wrote:
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 simulated_annealing.mode=first 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 convert_to_isotropic=true
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 ****************** REFINEMENT STATISTICS STEP BY STEP ****************** 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 ------------------------------------------------------------------------ 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.
Thanks,
Alejandro
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participants (2)
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alebus＠pasteur.edu.uy -
Pavel Afonine