#prosys dir prosys_dir = /home/chengji/software/prosys/ #modeller dir #modeller_dir = /home/chengji/software/modeller9v7/ modeller_dir = /home/tools/modeller-9.16/ #spem_dir spem_dir = /home/chengji/software/spem-release/ #compass dir compass_dir = /home/chengji/software/new_compass/ #hhsearch dir (old hhsearch) hhsearch_dir=/home/chengji/software/prosys/hhsearch #hhblits dir hhblits_dir=/home/chengji/casp8/hhblits/hhblits/ #atom dir atom_dir = /home/chengji/software/prosys_database/atom/ #muscle dir & lobster dir lobster_dir = /home/chengji/software/prosys/lobster/ #meta dir meta_dir = /home/chengji/casp8/meta/ #construct dir construct_dir = /home/chengji/casp8/construct/ #prc_dir prc_dir = /home/chengji/software/prc1.5.6/ #tm align program tm_align = /home/chengji/software/tm_align/TMalign_32 #number of templates to select (one model will be generate for each template) template_num = 10 #number of combined struture model to generate construct_num = 5 #time out (in seconds), set to 10 hours time_out = 36000 #number of threads used to generate alignments and models thread_num = 8 ##############the following options are copied from sp3 option###################### ##############many of them may not be useful######################################## #blast dir #blast_dir=/home/jianlinc/pspro/blast2.2.8 #blast_dir=/home/chengji/software/prosys/blast-2.2.9 blast_dir=/home/chengji/software/prosys/blast-2.2.17/bin #clustalw dir clustalw_dir=/home/chengji/software/prosys/clustalw1.83 #palign dir palign_dir=/home/chengji/software/prosys/palign/linux #tcoffee dir tcoffee_dir=/home/chengji/software/prosys/tcoffee2.03 #hmmer dir hmmer_dir=/home/chengji/software/prosys/hmmer2.3.2 #hhm prc dir prc_dir=/home/chengji/software/prosys/prchmm1.5.2 #pspro dir (should use pspro2) pspro_dir=/home/chengji/software/pspro2 #betapro dir betapro_dir=/home/chengji/software/betapro-1.0 ###################################################################### ##############Fold Recogntion Option################################## #fr option: input dir1 (hold template related files such as profiles) #template_dir=/home/baldig/jianlin/library template_dir=/home/chengji/software/prosys_database/library #fr option: fold recognition template library file (fasta format) #fr_template_lib_file=/home/jianlinc/prosys/library/lib/fr_set1 #fr_template_lib_file=/home/jianlinc/prosys/database/fr_lib/sort90 #fr_template_lib_file=/home/chengji/software/prosys_database/fr_lib/sort90 #fr_template_lib_file=/home/chengji/software/prosys_database/cm_lib/pdb_cm fr_template_lib_file=/home/chengji/software/prosys_database/cm_lib/pdb_cm_all_sel.fasta #fr_template_lib_file=/home/chengji/software/prosys_database/fr_lib/sort30 #fr_template_lib_file=/home/chengji/software/prosys/test/sort30 #fr_template_lib_file=/home/chengji/software/prosys_database/fr_lib/sort90 #fr_template_lib_file=/var/preserve/eval/fr_lib/sort90 #fr option: query dir: (hold query related files) #files needed: msa(align), chk, pssm, cm8a, cm12a, bcm8a, bcm12, bmap, hmm, set(9-line or more #used to store query related files (don't need to exist) #if query_dir is "generate", then the script of pairwise feature generation will automatically #generate query files and overwrite query dir. if not, it will use the files in the dir. #However: for fr_main_simple.pl and fr_main_simple_comb.pl, the query_dir will be overwritten #by output dir and all files are automatically regenerated. In that case, this option is not used. #query dir must use full path name # #Not used by the main scripts. 10/06/2005 query_dir=/home/cheng/prosys/system/test_fea/1aco-d1aco_1-query-bench #fr option: if use tcoffee in the feature generation(should always be 0) use_tcoffee = 0 #fr option: if use palign prof-prof alignment in feature generation (should always be 0) use_palign_prof = 0 #parameters exlusively used for palign or palign_ss profile-profile alignment #in fold recognition. Effective only for palign or palign_ss. #the gap below or equal to this value will be joined #in palign or palign_ss alignments for the same template fr_palign_join_gap_size=10 #the threshold to stop combine palign local alignments #fr_palign_stop_gap_size=20 fr_palign_stop_gap_size=10 #the threshold of selecting alignments of covering gaps #fr_palign_min_cover_size=20 fr_palign_min_cover_size=10 #fr option: number of templates to select (used by fr_main_simple_comb.pl/fr_main_simple_adv.pl) #But the program will automatically select all positive templates, but #limited by at most 50. #hard coded in fr_main_align_join.pl and fr_main_adv_comb_join.pl fr_temp_select_num=10 #fr option: number of combined alignments and structures to generated. #must be less than fr_temp_select_num fr_stx_num=10 #fr option: minimum cover size of choosing a template for alignment combination #fr_min_cover_size=20 fr_min_cover_size=5 #fr option: gap stop size. if gap is less than this number, the combination of alignment stops. #fr_gap_stop_size=20 fr_gap_stop_size=5 #fr option: maximum linker sized added to the segments of filling gaps fr_max_linker_size=10 #fr_option: alignment combination method (not applied to fr_main_simple.pl) #only be used by script: fr_main_adv_comb.pl so far. #advanced:advanced combination, simple:simple combination. fr_align_comb_method=advanced #fr_align_comb_method=simple #option for advanced combination only #<0: don't join the adjacent fragments(no gaps) #>=0: join adjacent fragments (allow gaps) #this option controls the maximum allowed intermedite #regions betweew two fragments for joining. adv_comb_join_max_size=15 #choose which alignment method is used as the basis of structural features #support two methods: clustalw and lobster #fr_stx_feature_alignment=clustalw #fr_stx_feature_alignment=lobster #fr_stx_feature_alignment=lobster_sel #fr_stx_feature_alignment=muscle fr_stx_feature_alignment=lobster_no_clustalw #option to decide if very significant svm models should be combined #recommended value: 0.7 or 0.5 #a large number such as 100 means no combination svm_comb_threshold=0.7 #################################################################################### ###########################Modeller Option########################################## #Modeller Options: #atom dir (the directory of storing atom files of templates for Modeller) #each template should have a file there named as: temp_name.atom.gz #atom_dir=/home/jianlinc/prosys/database/atom atom_dir=/home/chengji/software/prosys_database/atom #used by modeller: comparative modelling seq dir(11 line sequence format) #This directory is used by both fold recognition and CM. #cm_seq_dir=/home/jianlinc/prosys/database/seq cm_seq_dir=/home/chengji/software/prosys_database/seq #modeller option: number of models to simulate in modeller for each pir alignment #for each alignment, modeller will generate this number of models #and pick one with the minimum energy. #num_model_simulate=10 num_model_simulate=5 #################################################################################### ##########################Options for sorting blast local alignment########### #The file containing resolution/method/match ratio for all chains #chain_stx_info=/home/jianlinc/prosys/database/cm_lib/chain_stx_info chain_stx_info=/home/chengji/software/prosys_database/cm_lib/chain_stx_info #resort blast local alignment according to stx quality. #yes: resort, no: don't sort sort_svm_rank=no #ratio of evalue to be considered in resorting (must > 1). #only be valid if sort_blast_align is set to yes. #only if the ratio of two evalues is between 1 and ratio to #be considered for exchanging positions. #smaller, more strict. sort_svm_detal_rvalue=0.1 #ratio of resolution difference for being considered exchange. #in Angstrom. #only valid if sort_blast_align is set to yes. sort_svm_delta_resolution=2 #Option for adding stx information and remove identical by resolution #yes: do it. no: don't. fr_add_stx_info_rm_identical=no #resolution difference that decide if the redundant alignment will #be removed. bigger, more strict. fr_rm_identical_resolution=2 ###############################End of sorting and stx information option####### psipred_dir=/home/chengji/software/psipred/ new_hhsearch_dir=/home/chengji/software/hhsearch1.2/linux32/ #query-template alignment method #use spem to do alignment #alignment_method=lobster alignment_method=muscle