ó ±™xTc@ sddlmZddlZddlmZmZddlZddlm Z m Z ddl m Z ddl ZddlZejjddeƒZeZejd„Zd „Zdeejd „Zd „Zd e jfd „ƒYZd„Zedkreej dƒndS(iÿÿÿÿ(tdivisionN(t get_fp_fdptget_residues_and_ha(tSorrytnull_out(t runtime_utilssy crystal_info { resolution = None .type = float .help = Optional high-resolution limit. If specified, the calculation is only carried out at this resolution .short_caption = High-resolution limit .style = resolution .input_size = 64 seq_file = None .type = path .help = "Optional sequence file (1-letter code)." "Separate chains with a blank line or line starting with >." .short_caption = Sequence file .style = bold file_type:seq input_file chain_type = *PROTEIN RNA DNA .type = choice .short_caption = Chain type .help = Chain type (PROTEIN RNA DNA). This is used to estimate the number of atoms from the number of residues solvent_fraction = 0.5 .type = float .short_caption = Solvent fraction .help = Optional estimate of solvent fraction in your crystals .input_size = 64 residues = None .type = int .short_caption = Number of residues .help = The number of residues in the molecule or asymmetric unit. Note that it is the ratio of residues to anomalously-scattering atoms that matters. .input_size = 64 atom_type = None .type = str .short_caption = Anomalously-scattering atom .help = Optional name of anomalously-scattering atom. If supplied, you also need to supply the wavelength for X-ray data collection. If not supplied, then you need to supply a value for f_double_prime. .style = renderer:draw_phaser_scatterer_widget .input_size = 64 number_of_s = None .type = int .short_caption = Number of S atoms .help = You can specify the number of S atoms in the asymmetric unit. Only used if include_weak_anomalous_scattering=True. If not set, the number is guessed from the sequence file if present. f_double_prime = None .type = float .short_caption = F-double-prime .help = F-double-prime value for the anomalously-scattering atom. Alternatively you can specify the atom type and wavelength. .input_size = 64 wavelength = None .type = float .short_caption = Wavelength .help = Wavelength for X-ray data collection. If supplied, also specify the atom_type. Alternatively you can specify the value of f_double_prime .input_size = 64 sites = None .type = int .short_caption = Number of anomalously-scattering atoms .help = The number of anomalously-scattering atoms in the molecule or asymmetric unit. Note that it is the ratio of residues to anomalously-scattering atoms that matters. .input_size = 64 occupancy = 1 .type = float .short_caption = Occupancy of anomalously-scattering atoms .help = Estimate of occupancy of anomalously-scattering atoms } i_over_sigma = None .type = float .short_caption = I/sigI .help = Optional I/sigI. If supplied and resolution is supplied, the expected values of half-dataset correlation and cc*_ano based on this I/sigI and resolution will be calculated. target_signal = 30. .type = float .short_caption = Target anomalous signal .help = The anomalous signal that you would like to obtain. The value of I/sigma will be adjusted to obtain this signal. Typically you will need a signal of 15-30 so solve the substructure. min_cc_ano = 0.15 .type = float .short_caption = Target minimum anomalous correlation .help = You can set the target minimum (true) anomalous correlation (CC*_ano). This value affects the phasing accuracy after the substructure is determined. ideal_cc_anom = 0.75 .type = float .short_caption = Anomalous correlation with perfect data .help = The ideal_cc_anom is the expected anomalous correlation between an accurate model with isotropic anomalous scatterers and perfectly-measured data. The ideal_cc_anom is determined empirically. It is typically not unity because anomalous scatterers may have multiple locations with low occupancy or may be non-isotropic. A value of about 0.75 is a reasonable guess. include_weak_anomalous_scattering = True .type = bool .short_caption = Include weak anomalous scattering .help = At longer wavelengths the scattering of C, N, and O become significant relative to S. Default is to consider the scattering from C, N, O as noise. Additionally, (see intrinsic_scatterers_as_noise) if intrinsic anomalous scatterers (P and S) are weak, they will be counted as noise. This weak anomalous scattering is effectively noise and has the same effect as the ideal_cc_anom but it can be calculated from the composition. Its effects are added to those modeled by the ideal_cc_anom parameter. intrinsic_scatterers_as_noise = None .type = bool .short_caption = Intrinsic scatterers as noise .help = Applies if include_weak_anomalous_scattering=True. You can choose to treat any intrinsic scatterers (S for protein, P for nucleic acid) as noise, just like any contributions from C, N, or O atoms. This is default if anomalous scattering (f-double-prime) from these atoms is less than half that of your specified anomalous scatterer. Alternatively these atoms are excluded from the noise calculation and are assumed to be included in the number of sites you specify. control { show_summary = False .type = bool .help = Show summary only .short_caption = Show summary only verbose = False .type = bool .help = '''Verbose output''' .short_caption = Verbose output } tprocess_includescC sZtjjd|dtddƒ}|jjƒ}|dIJtjd|ƒjd|ƒ|S(Ntargst master_philt seq_file_defscrystal_info.seq_files Plan a SAD experiment t python_objecttout(tiotbxtphiltprocess_command_line_with_filesRtworktextracttformattshow(RR t command_linetparams((sT/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/plan_sad_experiment.pyt get_params¨s   cC sƒ|jjsBtd|jjd|jjd|ƒjƒ|j_n|jjrtjj |jjƒrt |jj|jj|jj d|ƒ\}}}|jj sÂ|d|IJ||j_ n|jj së|d|IJ||j_ n|jjsI|dd|IJ||j_qIn.|jj dkrI|jrItdd ƒ‚n|jj sdtd ƒ‚n|jjstd ƒ‚ndS( Nt atom_typet wavelengthR s-Number of residues based on sequence file: %ds,Number of S atoms based on sequence file: %ds0Number of sites for anomalously-scattering atom sbased on sequence file: %ds-Sorry need a sequence file or number_of_s if s' include_weak_anomalous_scattering=Trues4Please specify number of residues or a sequence files?Please specify number of sites or a sequence file and atom_type(t crystal_infotf_double_primeRRRtfdptseq_filetostpathtisfileRt chain_typetresiduest number_of_stsitestNonet!include_weak_anomalous_scatteringR(RR R R"R!((sT/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/plan_sad_experiment.pyt setup_params²s>  $           c!C s|st|d|ƒ}nt|d|ƒtjjjd|jjd|jjd|jj d|jj d|jj d|jj d|jj d |jjd |jd |jd |jd |jjd|jjd|jd|jd|jƒ}|jjr|jƒn|jd|ƒSdS(NR RR R!tsolvent_fractiontnsitesRRtfppt target_s_anot i_over_sigmat min_cc_anotdmint occupancyt ideal_cc_anomR$tintrinsic_scatterers_as_noise(RR%tmmtbxtscalingtplan_sad_experimenttestimate_necessary_i_sigiRRR R!R&R"RRRt target_signalR*R+t resolutionR-R.R$R/tcontrolt show_summaryR(RRt return_planR tplan((sT/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/plan_sad_experiment.pytrun×s.                  cC st|dtƒƒS(NR (R%R(R((sT/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/plan_sad_experiment.pytvalidate_paramsôstlaunchercB seZd„ZRS(cC st|jdtjƒS(NR (R:Rtsyststdout(tself((sT/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/plan_sad_experiment.pyR:øs(t__name__t __module__R:(((sT/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/plan_sad_experiment.pyR<÷scC s ggfS(N((tresult((sT/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/plan_sad_experiment.pyt finish_jobûst__main__i(!t __future__Rt!mmtbx.scaling.plan_sad_experimentR0RRt iotbx.philR t libtbx.utilsRRtlibtbxRtos.pathRR=R tparsetTrueRt master_paramsR>RR%R#tFalseR:R;ttarget_with_save_resultR<RCR@targv(((sT/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/command_line/plan_sad_experiment.pyts$     ™ %