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WHERE MRModel_id=?sUPDATE TemplateRMSTbl SET CCglobal=?, CCmap%d=?, CCpdb%d=?, MLAD%d=?, LLGensmbl%d=? WHERE MRModel_id=?sUPDATE MRModelTbl SET ModelResolution=?, SequenceIdentity=?, SSMseqid=?, ModelCompleteness=?, FullModelCompleteness=?, ClustalWlength=?, SSMlength=?, Annotation=?, ModelSCOPid=?, NumberofUniqueModelSCOPids =?, ModelClass=?, ModelFold=?, ModelSuperfamily=?, ModelFamily=? WHERE ROWID=?s*UPDATE MRModelTbl SET %s=%d WHERE ROWID=%di ssINSERT INTO ELLGtbl (MRModel_id, eLLGtarget, achievedELLG, LLGachievedres, LLGfullres, TFZfullres, TFZachievedres, sQfoundit, vrmsachievedres, achievedresol, foundit2) VALUES (?,?,?,?,?,?,?,?,?,?,?)iiis9Solution file has %d components of %s but %d is expected.s/UPDATE MRModelTbl SET TFZequiv=? WHERE ROWID=?sZUPDATE MRModelTbl SET TFZequiv%s=? WHERE MRTarget_id=? AND Fullmodel=? AND PartialModel=?s3UPDATE MRModelTbl SET SolutionRank=? WHERE ROWID=?s^UPDATE MRModelTbl SET SolutionRank%s=? WHERE MRTarget_id=? AND Fullmodel=? AND PartialModel=?sINSERT INTO AnnotationTbl (MRTarget_id, MRModel_id, Tstar, RFZ, TFZ, PAK, CCglobal, LLGfullres_vrms, LLGfullres_refl_vrms, iLLG, iLLGvrms, LLGvrms, LLGrefl_vrms, VRMSfullres, FracvarVrmsfullres) VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)s2SELECT COUNT(*) as total_record FROM AnnotationTblsiUPDATE AnnotationTbl SET CCmap%d=?, CCpdb%d=?, MLAD%d=?, LLGensmbl%d=? WHERE ROWID=?s_UPDATE AnnotationTbl SET vrms%d=?, Bfac%d=?, fracvarvrms%d=? WHERE ROWID=?stUPDATE MRModelTbl SET RFZ%d=?, TFZ%d=?, PAK%d=?, LLG%d=?, iLLG%d=?, LLGreflection%d=? WHERE ROWID=?s4UPDATE MRModelTbl SET iLLGfullres%d=? WHERE ROWID=?sVUPDATE MRModelTbl SET iLLG%s=? WHERE MRTarget_id=? AND Fullmodel=? AND PartialModel=?sVUPDATE MRModelTbl SET TFZ0%s=? WHERE MRTarget_id=? AND Fullmodel=? AND PartialModel=?sYUPDATE MRModelTbl SET Foundit%s=? WHERE MRTarget_id=? AND Fullmodel=? 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Will try downloading from the RCSB...shttp://www.pdb.org/pdb/files/rs sf.ent.gzstmp.gztwbsWriting tmp.gzRsWriting tmp.cifstmp.cifs --symmetry=..s.pdbs--output-file-name=sExecuting command: sNo mtz file available!i*s=Only intensities available in %s. Converting to amplitudes...s _I2ampl.mtzs--write-mtz-amplitudess--mtz-root-label=FOBSs --label=%ss--mtz=%ss%ssreflection_file_converter targssbSome reflections from the conversion %s have amplitude values of zero. Must massage intensities...s_mssg_I2ampl.mtzs--massage-intensitiess:Neither intensity nor amplitude columns seem present in %si)sWriting base input.txt file in s input.txts exists and will be overwritten.sHKLIN s LABIN I = s SIGI = s LABIN F = s SIGF = s(COMPOSITION PROTEIN SEQUENCE Phaserinputs NUM 1 s..is_BLASTchain_ids.txts* Subfolders now set up for MR calculationss-_BLASTchain_ids.txt lists model pdb_chain idss4with sequence identity and the permuted MR searches.s0input.txt is toplevel MR input to be joined withs)modelinput.txt before each MR calulation.s Done with BLASTnSetupMRruns.(?R.RURRLRRRRR2t LOG_FILENAMER/R0RuRR)RmRRRRRRRRRRiRKR RRFRRRRRwR7R(RRRRRRRRRRRhtshutiltcopyfiletFATALRDRRRR=RNRRRRORR(5R"RRRRtnoRNPRt reposfileRRRtatbtctmdlistRR<RtseqfnameR&Rt localmtznameR>RtcifgztgzfileRtcifdataRRRtSigcolRtSigIcoltmtzwithamplnametintensity2amplargt FcolI2ampt SigcolI2ampt IcolI2amptmtzwithmssgamplnametinfnamet inputfiletmtzstrtpreparedmodelsRRRtpsearchR1RRRtblastout((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/phaser/BLASTnMRfunc.pytBLASTnSetupMRrunss6+        8     /! &        ) 0(     0#   #    8    (%       : $cICs ddl}tdd}|jd|j|jf|jtjj|j |jd}|j ||j j t jd|j|jftjj|j |j|jd}t|}tt|dj} g} |tkr^|j} tt| d } xtd | D]} | | d }| | d d }|j j t jd ||ft|d}|j}|jtg|f}x+|jD]}|d j|jqW| j|q%Wtj|j tj}tjd |jjd}t|}tj j!d|}|j"j#}|j$j%j&}|j$j%j'}tt(j)|d }|j*d j+}d|d |d |d |d|d|df}|j*d j,j-t|j"j.}t|j/|j0d j1}ddddg}ttjj|j2ddj} t3j4d|jd| t3j5}!|!dkr|!j7}"t8|"d dt8|"d dt8|"ddt8|"ddg}nttjj|j2ddj}#t3j4d|jd|#t3j5}!|!dkrUd }$q^d }$n|j9|}%|%j:|_;|j;j<d|j;j<d|j;j<d|j;j<d|j;j=}&t>}'x(|&D] }(|(d dkrt}'PqqW|'r dd d!d"d#d$d%d&d'd(})|j;j<|)d)d*d+d,d-d.d/d0d1d2d3})|j;j<|)x,| D]$}*d4|*d })|j;j<|)qWd5d6d7d8d9})|j;j<|)d:d;})|j;j<|)d<d=d>})|j;j<|)nt| d d }+x9t|+D]+},|'r+d?|,})|j;j<|)d@|,})|j;j<|)dA|,})|j;j<|)dB|,})|j;j<|)dC|,})|j;j<|)dD|,})|j;j<|)|j;j<dE|,dF|,})|j;j<|)dG|,})|j;j<|)dH|,})|j;j<|)dI|,})|j;j<|)dJ|,})|j;j<|)dK|,})|j;j<|)dL|,})|j;j<|)dM|,})|j;j<|)dN|,})|j;j<|)dO|,})|j;j<|)dP|,})|j;j<|)dQ|,})|j;j<|)dR|,})|j;j<|)dS|,})|j;j<|)q+q+W|'r0 t|d kr0 x|d D]}-|-d }.dT|.})|j;j<|)dU|.})|j;j<|)dV|.})|j;j<|)dW|.})|j;j<|)dX|.})|j;j<|)dY|.})|j;j<|)q}Wntj|j |j|jdZ}/t|/d}0|0j}1|0jt?j?|j |}2|j@|j}3dg}4dg}5dg}6dg}7d g}8|tkrP tjtj|j d tAjAd[}9d }:x6|9D].};t|;dj}<|:tBjC|<7}:q Wtj|x|D]}-|-d }=|-d }.|=d\krV tg}>x| D]}?d\}@g|?d D]#}Ag|AD]}B|Bd ^q ^q d }Cd]j|C}Dx]tD|?d D]K\} }E|E|>kr |>j|Etg}Fd\g}G|2jE|G|E|F|1r# y|=d\krm |2jF|Gd |E|=}Hn|2jF|Gd |E}H|2jG|jH|?|D|E| |2jG|.|3||||||H| |4|5||$|6|7|:|||8Wq# tIk r }!|j j t jJtK|!d^tLjMq# Xnt|?d | d }+q q Wq WqV qV Wn|%jN|j;j|j j t jd_|dS(`NisBLASTMRcalculations.txtsa+s,%s, %s, in CollateMRautoResultsFromlistFile s MRResults.logs9CollateMRautoResultsFromlistFile, pdb: %s, calclabel: %s s_BLASTchain_ids.txtRiiis5MR models matching PDB ids in %s will be tagged as %sR*s.mtzR s#%3.3f %3.3f %3.3f %3.3f %3.3f %3.3fiiigs Rfactors.txtRs) (.*) (.*) (.*) (.*) (.*) seds_holdings.txts) sPRAGMA synchronous = OFFsPRAGMA journal_mode = MEMORYsPRAGMA cache_size=200000s"select tbl_name from sqlite_mastert MRTargetTblsBcreate table MRTargetTbl (p_id integer primary key autoincrement, s=TargetPDBid text, SCOPid text, icerings int, twinLtest real, s>NumberofUniqueSCOPids int, TargetClass text, TargetFold text, s<TargetSuperfamily text, TargetFamily text, Spacegroup text, sASpacegroupnumber int, IsPolarSpacegroup int, Crystalsystem text, s:IsigIgrt3res real, hires real, lowres real, outliers int, s:Resolution real, Unitcell text, MatthewsCoefficient real, s>NumberofResiduesinTarget int, WilsonB real, WilsonScale real, s<Robs real, Rall real, Rwork real, Rfree real, EDSentry int, sNTargetScattering int, UsedReflections int, Allreflections int, ASUVolume real)s@create table MRModelTbl (p_id integer primary key autoincrement,s.MRTarget_id int, Fullmodel text, Comment text,s0ModelOrder int, Foundit int, PartialModel text, s<ModelResolution real, SequenceIdentity real, SSMseqid real, sRNumberofResiduesinModel int, SolutionRank int, ClustalWlength int, SSMlength int, sEFullModelCompleteness real, ModelCompleteness real, Annotation text, s8C_L_rms real, SSMrms real, NewRMSD real, TFZequiv real, s Fracvar real, ModelSCOPid text, s1NumberofUniqueModelSCOPids int, ModelClass text, s9ModelFold text, ModelSuperfamily text, ModelFamily text, s CPUtime real)s(alter table MRModelTbl add column %s intsHcreate table AnnotationTbl (MRTarget_id int, MRModel_id int, Tstar int, sCRFZ real, TFZ real, PAK real, LLGfullres_vrms real, iLLGvrms real, sALLGreflection real, LLGrefl_vrms real, iLLG real, CCglobal real, s)LLGvrms real, LLGfullres_refl_vrms real, s*VRMSfullres real, FracvarVrmsfullres real)sMcreate table TemplateRMSTbl (MRTarget_id int, MRModel_id int, CCglobal real, sERefinedModel text, LLGvrms real, iLLGtemplate real, LLGreflvrms real)sJcreate table ELLGtbl (MRModel_id int, eLLGtarget real, achievedELLG real, sLLLGachievedres real, LLGfullres real, TFZfullres real, TFZachievedres real, sDfoundit int, foundit2 int, vrmsachievedres real, achievedresol real)s,alter table MRModelTbl add column RFZ%d reals,alter table MRModelTbl add column TFZ%d reals,alter table MRModelTbl add column PAK%d reals,alter table MRModelTbl add column LLG%d reals6alter table MRModelTbl add column LLGreflection%d reals-alter table MRModelTbl add column iLLG%d reals4alter table MRModelTbl add column iLLGfullres%d reals1ALTER TABLE AnnotationTbl ADD COLUMN CCmap%d reals1ALTER TABLE AnnotationTbl ADD COLUMN CCpdb%d reals0ALTER TABLE AnnotationTbl ADD COLUMN MLAD%d reals5ALTER TABLE AnnotationTbl ADD COLUMN LLGensmbl%d reals0ALTER TABLE AnnotationTbl ADD COLUMN VRMS%d reals0ALTER TABLE AnnotationTbl ADD COLUMN Bfac%d reals7ALTER TABLE AnnotationTbl ADD COLUMN FracvarVrms%d reals2ALTER TABLE TemplateRMSTbl ADD COLUMN CCmap%d reals2ALTER TABLE TemplateRMSTbl ADD COLUMN CCpdb%d reals1ALTER TABLE TemplateRMSTbl ADD COLUMN MLAD%d reals6ALTER TABLE TemplateRMSTbl ADD COLUMN LLGensmbl%d reals1ALTER TABLE TemplateRMSTbl ADD COLUMN VRMS%d reals1ALTER TABLE TemplateRMSTbl ADD COLUMN Bfac%d reals8ALTER TABLE TemplateRMSTbl ADD COLUMN FracvarVrms%d reals1alter table MRModelTbl add column TFZequiv%s reals-alter table MRModelTbl add column TFZ0%s reals-alter table MRModelTbl add column iLLG%s reals0alter table MRModelTbl add column Foundit%s reals4alter table MRModelTbl add column SolutionRank%s ints1alter table MRModelTbl add column CCglobal%s reals_DoneMRJobs.txts*.seqRRs s Results written to (Otsqlite3RRR.RURR/R0RuR2RRmRRRR RRR=RRdRRRARoRRR)R(RRRRRt space_grouptcrystal_systemtspace_group_infoRt lookup_symboltnumberRt list_originstcrystalstunit_cell_parameterst unit_celltvolumetall_opsRRtextract_valuesRvRXRR\RERRStconnecttcursorRSRtfetchallRFt BLASTMRutilsRR*R 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