xTc @ s:ddlmZddlZddlmZddlmZmZddl m Z ddl Z ddl Z ddl Z ddZddZd d d dd Zd ddddddddedd ZdddddddZdddddddZddZdddddddZdZdZddddddedZdde jdZdde jdZdZddddde jdZdde jdZ ddZ!d d!Z"dd"ddddddd#e jd$ Z#ggggd"d%Z$d&ej%j&fd'YZ'dS((i(tdivisionN(tany_sequence_format(tSorrytnull_out(t table_utilstPROTEINcC s|dkrd}nd}|S(NRg`@g~@((t chain_typetvol_per_residue((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pytget_vol_per_residue s  cC s|dkrd}nd}|S(NRii((Rtatoms_per_residue((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pytget_atoms_per_residues  ig@g?cC s/d|td|d|d|d}|S( Ng@gn! @gioT?Rg?ign!@gQD|@(R(tresiduestdmintsolvent_fractionRtnrefl((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pyt get_nrefls+g.@igffffff?cC sd}d}d}|r!d}nxt||D]}|dt|}t||||||d|d| d| d| d| d | d t\}}}}}}}|dk r||krq1n||d }|dks||kr1|}|}q1q1W|dkrt||||||d|d| d| d| d| d | d t\}}}}}}}t|||||d ||d |d|d|d| d| d| d| d | dt }n|S(Niig?tfa2tfb2tdisorder_parametertfo_listtfo_number_listt occupancyt get_fpp_weakit target_s_anotntriest min_cc_anot include_zero(tNonetxrangetfloattget_values_from_sigftFalsetget_sigf(RtnsitestnatomstztfppRRRRRRRRRRtratio_for_failuret closest_sigft closest_dist2t start_valuetitsigfts_anotcc_anotcc_halftfpp_weakt cc_ano_weakt cc_half_weakt i_over_sigmatdist2((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pyR s<    c C s^t||||||d|d|d|d| d| d| } | tjd ||} | S( NRRRRRRg@g@g?(t get_cc_anotmathtsqrt(RR!R"R#R$R*RRRRRRR,tsano_new((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pytget_sanoCs c  C sh|g} |g} td| d| d| d| d| }dd||||d|}tj|S(s0cc_ano**2=1/[1 + /(n/N)(Za/Z)**2]tfpp_listtfpp_number_listRRRg?i(tget_normalized_scatteringR4R5(RR!R"R#R$R*RRRRRRttarget_fpp_listttarget_fpp_number_listt local_fa2t ccano2_new((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pyR3_s   "cC s-td||d|}|d|}|S(s)cc_half=cc_ano_perf**2/(2-cc_ano_perf**2)g?ig@(tmin(R,Rtccano2t cc_half_new((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pyt get_cc_halfusc C st||||||d|d|d|d| d| d| } | d} d}xtd d D]{}t|d }t|||||||d|d|d|d| d| d| }|| kr_||kr_|}Pq_q_W||S( NRRRRRRg@g?iieg{Gz?(R7RR(RR!R"R#R$R*RRRRRRtsanottargett best_scaleR)tscaletss((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pytestimate_fpp_weaks cC s|dkrd|SdSdS(Nig)\(?g8@((R*((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pytget_i_over_sigmas cC s#|dkrd|}nd}|S(Nig)\(?gMbP?((R1R*((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pytget_sigf_from_i_over_sigmas  c C sht||||||d|d|d|d| d| d| } t||||||d|d|d|d| d| d| }t|d|}| rKt||||||d|d|d|d| d| d| }t||||||d|d|d|d| d| d| }t|d|}t|}| ||||||fS| |||||dfSdS(NRRRRRRg(R7R3RBRHRI(RR!R"R#R$R*RRRRRRRR+R,R-R.R/R0R1((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pyRs&   cC s{| s| r!tddnddlm}y"|j|}|j|}Wn!tk rvtd|nX|S(Ns(Please specify either f_double_prime or satom_type and wavelengthi(tsasakis'Unable to get scattering factors for %s(Rt cctbx.eltbxRKttablet at_angstromt ValueError(t atom_typet wavelengthtoutRKRMtfp_fdp((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pyt get_fp_fdps  cC sx| s| r!tddnddlm}y|j|}|j}Wn!tk rstd|nX|S(Ns(Please specify either f_double_prime or satom_type and wavelengthi(RKs'Unable to get scattering factors for %s(RRLRKRMt atomic_numberRO(RPRQRRRKRMtfo((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pytget_fos  cC sO|jjdd}t|}|jd}|jd}|||fS(Nt ttMtC(tuppertreplacetlentcount(tsequencetn_aatn_mettn_cys((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pytget_aa_and_mets  iic C sNd}|dkr%|dIJd}n|jd krMtd||}n|jdkrtd|||}||tt|d}nu|jdkr|tdtddtt|d }n0|tdtd dtt|d }|r/|d |j|fIJn|dkrD|}n||fS(Ns-No heavy atom type set, so no sites estimatedtseitsg@tbrR)i g4@igY@s% Best guess of number of %s sites: %d(Re(Rf(RgR)(RtlowertmaxtintRR?R\(RPRbRcRat ncs_copiesRRtnumber_of_sites_lowrestnumber_of_sites((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pytget_number_of_sitess$   !30 c C s| stjj| r)tdnt|\}}|rTtd|nd \}}}xG|D]?} td| j\} } } || 7}|| 7}|| 7}qjW||} td|d|d|d|d d d t\}}||| fS( Ns3Please supply number of residues or a sequence files*Sorry, unable to read the sequence file %siR`RPRbRcRaRkiRR(iii( tostpathtisfileRRRdR`RnR(tseq_fileRPRRRtobjectst non_compliantRaRbRctseq_objtn_aa_tn_met_tn_cys_t number_of_sRmRl((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pytget_residues_and_has     cC s$|s dS|d}d||SdS(Ngig?((t ideal_cc_anomtcc2((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pytget_disorder_parameter s g?cC s]t}xB|D]:}td|d|j}|||kr t}q q W|rUtStSdS(NRPRQ(tTrueRTtfdpR(tintrinsic_scatterers_listt target_fppRQt minimum_ratiotall_weaktxR$((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pytinclude_intrinsic_scattererss  g?gc C s|dkr\dg} |dkr.d|}n||g} dddg} ddd g} nOd g} d g} dddg} d d dg} |dkr| dcd 7/ needed to obtain anomalous signal of 15-30s(Targets for entire dataset)is0SAD solution unlikely with the given parameters.s Anomalous Useful Useful Half-dataset Anom CC Anomalous Dmin Nrefl I/sigI rms(sigF)/ CC (cc*_anom) Signal rms(F) (%) s %s %s %s %s %s %s %sRtcolumn_headerstd_mintNreflsI/sigIsrms(sigF)/rms(F) (%)sHalf-dataset CC_anosCC*_anos Anom. signals Note: Target anomalous signal not achievable even with very high I/sigma for resolutions of %5.2f A and lower. I/sigma shown achieves about %3.0f%% of maximum anomalous signal. sS Note: No plausible values of I/sigma found for resolutions of %5.2f A and lower. s This table says that if you collect your data to a resolution of %5.1f A with an overall / of about %3.0f then the half-dataset anomalous correlation should be in the range of %5.2f - %5.2f. This should lead to a correlation of your anomalous data to the useful anomalous differences (CC*_ano) in the range of %5.2f - %5.2f and a useful anomalous signal around %3.0f - %3.0f, where an anomalous correlation of about %5.2f and an anomalous signal of 10-15 should be sufficient to find the substructure and calculate phases. g@sX The value of rms(sigF)/rms(F) is approximately the inverse of I/sigma. The calculations are based on rms(sigF)/rms(F). Note that these values assume data measured with little radiation damage or at least with anomalous pairs measured close in time. The values also assume that the anomalously-scattering atoms are nearly as well-ordered as other atoms. If your crystal does not fit these assumptions it may be necessary to collect data with even higher I/sigma than indicated here. Note also that anomalous signal is roughly proportional to the anomalous structure factors at a given resolution. That means that if you have 50% occupancy of your anomalous atoms, the signal will be 50% of what it otherwise would be. Also it means that if your anomalously scattering atoms only contribute to 5 A, you should only consider data to 5 A in this analysis. sWhat to do next:st 1. Collect your data, trying to obtain a value of I/sigma for the whole dataset at least as high as your target.s2. Scale and analyze your unmerged data with phenix.scale_and_merge to get an accurate estimate of your half-dataset anomalous correlation and your estimated useful anomalous correlation cc*_anom.s3. Compare the half-dataset anomalous correlation and cc*_anom with the estimated values in the table above. If they are lower than expected you may need to collect more data to obtain the target half-dataset correlation and target anomalous signal. (t show_headertshow_sub_headertshow_paragraph_headertshow_preformatted_textt__dict__RPR$R4R5R!RttupleRRR^Rt show_textt gui_outputRt simple_tablet show_tableRRtsortR%RR(RRRttRtrowtfatfbtfabRMR R!RR$R1R*R0R-R/R,R+((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pyt _show_impl"s~              0  "    N(t__name__t __module__RR~RRRRRRRRRRRRRRRR(((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pyRfs@ r             ((t __future__Rt mmtbx.scalingtmmtbxtiotbx.bioinformaticsRt libtbx.utilsRRtlibtbxRR4tsysRoRR RRR~R R7R3RBRHRIRJRtstdoutRTRWRdRnRzR}RRR:tscalingtxtriage_analysisR(((sO/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/scaling/plan_sad_experiment.pyts^       #            /