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@WD$QD$$<$c*Y}`F9ut}׉]u}UVSfWɅ~fWYX@9uf([^UWV8EЉỦMȉe؍)ĉe$~NUЃ UE ~ uEԺY\B9uIGE 9}u‹UJUċEMЍD}^ЋEȋUD}Elj}܋UʉUM̍DEE+EHE}EĉEBUu9U~'uU}9Y\A;Muf(E^ƋUMHEămm mEue؍e^_UWVS[}~6EW((XXHXPB 9UuZZZ}fWf(f(*M^Z,f(Y\Au0@ , u@t@fWf.zt u '<$xDž t=QȹB^DBAuױ +f( fWҺtf(YLD\YXBuQf(fT[Ya^f. 't4$l {X$uBUD$D$ UD$OD$$$c$ 6uBUD$D$ UD$OD$$$cQFu$f$ uF$ uˋf(_f(Bu[fWf(ͺ9tfTXBu\]Auf(Xf(Yi^f(XBuDžD|x]QȺD^DBu$ yDžuBUD$D$ UUD$OD$$$c|fW҉( f(ʺDYDXBuꋍ( Fuf(DfWҺxf(YLD\YXBuQf(fT[Ya^f.D'<$Dt$Fu䋅$f(fW[Yf(Yf(Yf(YX\X f(Yf(Yf(\X@f(Yf(YXX`EEX\Y(f(Y\\XHYYf(\XhEE\X0XYP\XXpEEDž8Dž<DžXDž\DžxDž|EE?[WWW$D$D$<48 $D$D$v 񋅐MDžDž}} uDžfWHUT$D$GD$GD$ $CHLP\N\V\YYXYXZX 9EG*E^݅e[^_%s%s: cannot read 1st input file name %s: cannot read matrix (option -x) %d%s: cannot read P : type of analysis %f%s: cannot read gap open penalty (-G option) %s: cannot read gap extention penalty (-g option) %s: cannot read threshold (-W option) option -w: threshold is <= 0.0, setting it to %f %s: cannot read recovering ratio (-r option) option -r: recovering ratio is not in [0,1], setting it to %f %s: cannot read proba (-N option) option -N: proba is <= 0.0, setting it to %f %s: cannot read minimum score (-m option) %s: cannot read minimum rms (-M option) option -m: minimum rms is <= 0.0, setting it to %f %s: cannot read number of wanted best subalignments %s: subalignment number cannot be less than 1, setting it to %d %s: cannot read minimal length %s: minimal length cannot be less than 0, setting it to %d %s: cannot read number of shuffle %s: cannot read extend Cannot open out file (-i option) Cannot open error file (-j option) %s: cannot read maximum rrmsd a:b:D:e:Fg:G:hi:j:lL:m:M:n:N:pP:qr:s:u:UvVw:Wx:z%s: cannot read matrix in file %s ABCDEFGHIJKLMNOPQRSTUVWXYZBlosum62%s: cannot read matrix in file Blosum62 %s: option inexistante .set%s%s.pml%s:: error: No input 1st file ! exiting... rb%s:: error: cannot open %s %s:: error: cannot open temporary file %s:: Problem uncompressing 1st file %s, exiting.... -> 1st file uncompressed (%s) %s:: Problem uncompressing 2nd file %s, exiting.... -> 2nd file uncompressed (%s) Problem in reading protein structure in %s %d eme proteine , exiting...End of first database file, %d proteins have been read Problem in recoding protein %s angles exiting... **********Problem in reading sequence in %s %d th reading ... plus de %d residus, on passe a la suivante ... %s %d **************** reading %s temps %f num prot %d Problem in reading the %dth protein (ignored) End of second database file, %d proteins have been read Problem in recoding protein %s angles (ignored) ========Problem in reading sequence in %s %d th reading ...p0 : pb format binaire ...================ reading %s num prot %d probleme shuffle %s %s nmatch %d score : %f nb match %d threshold score=%f (ERR_SHUFFLE=%d) wtCan't open set file %s Print results for Gok in %s Can't open pymol file %s Print results for pymol in %s ************************no match Pb in reading %d sequences/structures Pb in recoding %d sequences/structures No protein read in one of the database file : file1 : %d file2 : %d ********** fin du fichier ************* sim.czpb malloc avec %s (%d %s) (size=%d) ACDEFGHIKLMNPQRSTVWYACGTsimalign:: not enough memory for RMS computations (pp0,pp1) simalign:: not enough memory for swres! DNA:3D-STRUCTURE:PROTEIN:%s: match %d mismatch %d gap-open %d gap-ext %d CCDDRRSSEEFFHHWWIIJJXXYYSsROWSIM: not enough memory for salign sROW[i]LISTLIST[i]--> K = %d Kwanted = %d There are no %d alignments between two sequences--> match count = %d score = %d probleme proba waterman_vingron break: limit score, probability or length given is reached added match (%4d,%4d) (%4d,%4d) (score=%.2f len=%d) alignment discarded too much overlap (%.3f), restarting... (%4d,%4d) (%4d,%4d) (score=%f len=%d) sim: break cause length (%d) < minlength (%d) sim: break cause score (%f) < minscore (%f) sim: break cause proba (%f) < proba limit (%f) sim: break cause number of matches reached sim: break cause no more matches sim: break unknown cause !!! swalign:: not enough memory for crossed rms swalign:: not enough memory for group swalign.cswresswres->posd0swres->posd1swres->posf0swres->posf1swres->scoreswres->score_freqswres->score_par_freqswres->score_GLswres->tm_scoreswres->score_blosangleswres->recoverswres->rmsswres->rev_rmsswres->saliswres->tProbaMTD_p0swres->tProbaMTD_p1swres->tProbaIndepswres->tProbaBiswres->alphaswres->betaswres->gammaswres->new_rmsswres->matrix4xswres->sali[swres->nmatch]MYFREE null %s%-6c: %6d %6d %7.1f - ##3 %4d - ---- p0= %s%c p1= %s%c RESULTS ---- ********************************************************* Number %4d local alignment Begins at (%d,%d) [PDB=(%4d%c,%4d%c)] Ends at (%d,%d) Length protein1 %4d protein2 %4d Score %10.2f Score/Alignement Length %8.3f RMS or Probability %7.2f Overlap %4.2f Alignment length %4d MTD Probability protein1 %4.3f protein2 %4.3f Zscore %.3f Blosum score: %5d GL score : %5.2f Group : %1d Score_freq : %20.2f Blosum_angle : %5.3f TM score %5.3f RRMSD: %.2f Sequence alignment corresponding to structure match: Sequence alignment: Angle alignment: NUM GROUP %7d %5d [%3d] %7.2f Sum Log MTD Probability protein1 %6.5f protein2 %6.5f @p0 p1 #repeat start0 start1 lg_prot score rms/proba overlap lg_match match1 match2 blosum GLscore compat start0 start1 end0 end1 RRMSD%10s%c %10s%c %6d %6d %6d %7d %8.2f %11.2f %11.2f %8d #1 #2 #3 %6d %7.2f %6d %4d %4d %4d %4d %6.2f ##1 %s%c %s%c %4d ##2 ==1 ==2 %6.1f*pp0*pp1swalign:: not enough memory for RMS computations (pp0,pp1) swalign:: not enough memory for swres! swalign::not enough memory for NewMatrix alignsw:: cc <%c> %f is not s,i or d, this should not append! alignsw:: lastmove <%c> is not s,i or d, this should not append! swalign2.calilensubpb realloc avec %s (%d %s) pp0pp1swalign2: not enough memory for RMS computations gap_extsIisJjgap_ext[j]sIi[j]sJj[j]best_scoresbest_scores[i]salign%s %s too much overlap (%.3f), restarting... (%4d,%4d) (%4d,%4d) (score=%.2f len=%d) pas de match score %f score=%15.2f (minscore=%15.2f) normalized score = %15.2f stop on match: step %d (nmatch=%d): score %.2f (min=%.2f) proba %.4f (lim=%.4f) len %d (minlen=%d) stop on score: step %d (nmatch=%d): score %.2f (min=%.2f) proba %.4f (lim=%.4f) len %d (minlen=%d) stop on proba: step %d (nmatch=%d): score %.2f (min=%.2f) proba %.4f (lim=%.4f) len %d (minlen=%d) stop on length: step %d (nmatch=%d): score %.2f (min=%.2f) proba %.4f (lim=%.4f) len %d (minlen=%d) pb dans aa3to1: %s, pos: %s, cases %d indice %d NewProt pb de mallocEnd of data file Cannot read binary file (is file really in binary format?) BinaryReadProtAlpha: cannot allocate for pProt pdb.entnb max de chaines/fragments (%d) depasse pour %s angle %f du residu %d de la proteine %s non valide, ignore BinaryReadProtAlpha:: debut frag 0 (frag %d) LitPdbProtAlpha:: Error: %s Pb in reading PDB file : residu null angle non valide: %f (%d) RecodeAngles:: pb de recodage, angle (%f) recode (%d) est > au maximum (%d) LitEnTete: pas de HEADER sur ligne [%s] LitEnTete: Fichier vide PATHLitEnTete: pas de PATH sur ligne [%s] NBRESLitEnTete: Cannot read number of residues LitEnTete: pas de NBRES sur ligne [%s] Problem in residue number reading in header End of file encountered while searching to read next header End of file encountered while reading header LitProtAlpha:: Empty file Problem in allocation for pProt in LitProtAlpha Incorrect number of residues: %d read residues over %d Problem with ReadPhipsiLine in LitProtAlpha Maximum number of chains/fragments (%d) exceeded for %s End of file reached nombre de residus incorrect: %d residus lus sur %d pb avec ReadPhipsiLine ds LitProtAlpha angle %f du residu %d de la proteine %s non valide , ignore not enought memory for temposeq (fasta) .. IO error 1 with sequence #%s IO error 2 with sequence #%s (flag ok 0) sequence non multiple de 3 !!! : %d Too much undefined characters in #%s not enought memory for pProt (fasta) .. Fin de ficher IO error 2 with sequence #%s (flag not ok) Pas de minimier a desallouer !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Results impredictable Minimier tree was sorted before all proteins were ranked %s%s%s%s!!!!!!!!!!!!!!! I think the score hasn't been computed: %f init_minimier:: Error: Not enough memory for result treer%d%d%s PAM %s Proximity %s Distance Matrix used : %s %s Vocabulary : %s %s Threshold : %d %s Values : %s %c %s %c %3d %s Classes : %s %c %s %c w%d %d %3d%4.2f Matrix file is not symetric Matrix values < minval or > maxval Bad matrix (similarity should be distance) bad type matrix simple_convert: no proper conversion indicated MAT%c %c %f --> Sum %c %f (proba simple %f) rtSet_TableFreq:: can't open %s for statistics ReadTable1Dim:: premature end of frequencies file bad format for number of groups in ReadTable1Dim <%s> stats.c*t1ReadTableFreq:: premature end of frequencies file %d %lfReadTableFreq:: bad format <%s> ReadTableFreq:: Cannot read line before 2-uple in frequency file *t2%d %d %lfReadTableFreq:: bad format (2) <%s> pb au recodage des angles dans CalculProbaBiAli, angleGroupe: %d, nbGroupes: %d lgMot: %d j: %d indxproblem in angle recoding in CalculProbaMtd avec %s indx[%d]= %d, max %d, angle %d (%d), : %f mot %d: %d a %d @ probabilites simples @ %20d%20d%3d %6d %10.2f %8.2f %10.2f %10.2f HEADER ZZZ %d %f %f %f Ecriture du fichier pour pymol impossibles (un des parametres est null) load %s.pdb , struct1 hide everything, struct1 show ribbon, struct1 color blue, struct1 load %s.pdb , struct2 hide everything, struct2 show ribbon, struct2 color red, struct2 select sel11, struct1 and resi %d-%d color forest, sel11 select sel12, struct1 and resi %d-%d color yellow, sel12 select sel21, struct2 and resi %d-%d color purple, sel21 select sel22, struct2 and resi %d-%d color orange, sel22 run fitting.py fitting struct1, i. %d-%d , struct2, i. %d-%d impossible d'afficher la proteine %d a parameter of EcritEnTeteSet is NULL name %s%d visible 1 color %d path %s adress %d end a parameter of EcritToutDansSet is NULL Cannot create "set" file *-PROTEIN-SET---ASCII-FILE--* * suite2 * END_PDB_REC un des parametres de EcritEnTeteSet est NULL Impossible de creer le fichier set name match%d pdbref 0 %d %c-%d %c %d-%d %d-%d pdbref 1 %d %c-%d %c %d-%d %d-%d symbol alpha END_WORD cant open file %s to readr+*Error* [%d] %s BUG: %s k-uple too big with this alphabetnot enough memory for hash table(i,j >= siz) in HashRandom(i >= siz) in DistribRandomswalign:: not enough memory for tempo file stat_sequences.c swalign:: not enough memory for temposeq Error in Shuffling: exit... (%d) wv1: score %f (%4d,%4d) (%4d,%4d) stats_sequence.cwater_vingscorebisscoresscores[i]nbscorebis[i]scores[j]Invalid arguments in routine GAMMQa too large, ITMAX too small in routine GCFx less than 0 in routine GSERa too large, ITMAX too small in routine GSER> Numerical Recipes run-time error... > %s allocation failure in vector()allocation failure in ivector()allocation failure in dvector()allocation failure 1 in matrix()allocation failure 2 in matrix()allocation failure 1 in dmatrix()allocation failure 2 in dmatrix()allocation failure 1 in imatrix()allocation failure 2 in imatrix()allocation failure in submatrix()allocation failure in convert_matrix() @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ @@@@@@@@@@ Parameters used : @@@@@@@@@@ @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ @@ Type of file : 3D amino acid sequences DNA sequences @@ File : %s format PDB fasta binary alpha @@ Number of alignments to show : %3d @@ Minimum score %5.2f @@ Gap penalty : opening : %3.2f + k * extension : %3.2f (k total gap length) @@ Overlap allowed : %2.3f @@ Algorithm : Huang-Miller @@ Algorithm : Smith-Waterman @@ maximum RRMSD %3.2f @@ Threshold for the score %5.2f @@ Minimum length for repeats : %d @@ P-value %5.2f @@ Declumping method : %d @@ Substitution matrix %s @@ Number of random sequences : %5d @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ %s: Usage: -s input_file -P [0|1|2] options ******************** FILES ********************************** -s file : file is in PDB format or fasta format for sequences ******************** STRUCTURE / SEQUCENCE ********************************** -P<0/1/2> 0 : structure analysis -P<0/1/2> 1 : proteique sequence analysis -P<0/1/2> 2 : nucleique sequence analysis ******************** OPTIONS ********************************** -l output on one line per match (several lines output by default) -n number of best subalignments to show (even if they are not statistically significant for sequences) - default for structure: %d - default for sequence: -1, i.e. the algorithm rely on statistical criteria for stopping output) -L minimal length for the repeat %d -m : minimum score for output subalignment -z : use default minimum score for output subalignment(def structure %.0f protein %.0f nucleic %.0f) -N : probability for dna and protein (def:%f) gaps : -G -1 : default value for gap open and extension penalty : %5.2f structure, %5.2f protein, %5.2f nucleic) default gap extention penalty : %5.2f structure, %5.2f protein, %5.2f nucleic) gap cost = gap_open + k * gap_ext (k being total gap length) -G : other value for gap open penalty -g : other value for gap extension penalty -r : ratio of tolerated recovering [0,1] (def:%4.2f) -q : output matches are sorted by scores (default: sort is done on RMS) -i : standard output -j : error output -W : Smith/Waterman algorithm is to be used (default: Huang/Miller algorithm) -F : No sequence/structure size limit, (default:%d when SW is used) ******************** OPTIONS FOR SEQUENCES ONLY ********************************** -x matrix (if amino acid or DNA sequence) -D : number of shuffled sequences used to calculate the statistical significance of the scores, default : %d -p second method of Waterman and Vingron for statistical significance : declumping estimation ******************** OPTIONS FOR STRUCTURES ONLY ********************************** -M : minimum rms for output subalignment(def:%f) -u : normalize minimum rms for output subalignment (Betancourt, Skolnick, 2001) (def:%f) -U use RMSD instead of Relative RMSD -w : value of threshold for angle score (def:%10.2f) note: score is detailed in paper -e : to extend alignment for amino acid distant than less than x Angstrom PrintArbreScan:: No protein returned from the minimier -------------------------------------- %s: CPU User Time : %8d sec %4d usec %s: mem size in Ko : ru_minflt:%d ru_majflt:%d %s: mem size in Ko : ru_maxrss:%d ru_ixrss:%d ru_idrss:%d ru_isrss:%d ru_minflt:%d ru_majflt:%d ru_inblock %d ru_oublock %d ru_nswap:%d no_nameprobleme ecriture binaire not enought memory for seq (fasta) .. fin du fichier !!! 1 IO error 1 with sequence #%s libfasta.cseq->seq2 IO error 1 with sequence #%s %d /UNK/ALA/CYS/ASP/GLU/PHE/GLY/HIS/ILE/LYS/LEU/MET/ASN/PRO/GLN/ARG/SER/THR/VAL/TRP/TYR/MSE/CSE/ASX/GLX/CEA/HYP/ACD/HSE/HYL/ALB/ARO/PCA/BAS/SAR/BET/TAU//ILE/LEU/ASP/ASN//CYS/SER/THR/VAL//GLY/ALA/%s new_residu:: not enough memoryput_atom_in_res:: not enough memoryset_residue_neighbours:: trop de voisinsCAget_CA_TFactor:%3s %4d has no CA atom get_CA_xyz:%3s %4d has no CA atom %s :: residue %s %4d %s residue %s %4d %s%s :: residue %s %4d %sget_distca_1_2:: residue does not existfollowingerreur distance : trou precedingget_phi_psi:: residue does not existCNget_chi:: residue does not existCBCGCG1OGOG1SGCDCD1OD1SDND1CECE1OE1NENE1get_alpha_tau:: residue does not exist%hdget_atom: bad atom format%creadPdbResidues: protein %s Cannot read key in line <%s> HEADERDESCCOMPNDSOURCEREMARK2 RESOLUTION.ATOMHETATMENDMDLENDTERlibphipsi.c*tChainpb malloc avec %s (%d %s) readPdbResiduesChain: protein %s Cannot read key in line <%s> EXPDTANMRTHEORETICAL%d chain Chain %d %c first res %d%c nbRes %d ReadPhipsiLine: no line %3s %hd%c %f %f %f %f %f %fReading input file with x y z %3s %hd%c %f %f %fReading input file without x y z ReadPhipsiLine:: Bad file format in <%s> readBinary: Cannot read header readBinary: Cannot read path readBinary: Cannot read number of residues readBinary: Not enough memory for binres array ! readBinary: Cannot read residues, %d residues expected, %d residus read! 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