############################################################################################################ #this text file includes the options used in comparative modelling used by cm_main_comb.pl (originally) ##the same settings are re-used by hhsearch-based template based approach (10/17/2007) ############################################################################################################ ###############################Software and Data Settings#################### #prosys script dir prosys_dir = /home/chengji/software/prosys/ #blast tool dir #blast_dir = /home/jianlinc/pspro/blast2.2.8/ blast_dir = /home/chengji/software/prosys/blast-2.2.17/bin #modeller 7.0 dir #modeller_dir = /home/chengji/software/prosys/modeller7v7/ #modeller_dir = /home/chengji/software/modeller9v7/ modeller_dir = /home/tools/modeller-9.16/ #formated pdb database dir #pdb_db_dir = /home/jianlinc/prosys/database/cm_lib/ pdb_db_dir = /home/chengji/software/prosys_database/cm_lib/ #pdb_db_dir = /var/preserve/eval/cm_lib/ #use non-redundant db dir (should always use non-redundant database) #nr_dir = /home/jianlinc/pspro/data/nr/ #nr_dir = /var/preserve/nr/ #nr_dir = /home/chengji/software/prosys_database/nr_latest/ nr_dir = /home/casp13/uniref/ nrdb = uniref90 #not use nr (should never choose this option. its performance is worse) #nr_dir = none #atom files dir #atom_dir = /home/jianlinc/prosys/database/atom/ atom_dir = /home/chengji/software/prosys_database/atom/ ###########new settings specifically for hhsearch profile-profile based approach #hhsearch dir hmmer_dir=/home/chengji/software/hmmer-3.0b3/binaries/intel-linux-x86_64 #all current templates hmmerdb=/home/chengji/software/prosys_database/cm_lib/pdb_cm #templates built before May 10, 2007 (CASP7 starts) #hhsearchdb=/home/chengji/software/prosys_database/casp7_hhsearchdb #meta dir #meta_dir=/home/chengji/casp8/meta/ meta_dir=/home/chengji/casp8/hmmer/ #common meta dir meta_common_dir=/home/chengji/casp8/meta/ ############################################################################### ############################End of Software and Data Settings################# #################################PDB blasting options####################### #Not used any more. evalue threshold for msa alignment generation. #Should we change it to 1.0? #this value is not used anymore. (collpased with cm_blast_evalue) #cm_align_evalue = 0.5 cm_align_evalue = 0.001 #evalue threshold for template blasting and selection on PDB. #Reasonable values: 1.0, 0.1, 0.01, 0.001. #psi-blast default evalue is 1.0. (-e option) #casp6, some paper suggest: 0.01. (we may choose this one) #cm_blast_evalue = 1.0 ############This e-value is used by sam too###################### #cm_blast_evalue = 0.001 cm_blast_evalue = 1 ################################################################# #number of iteration of blasting on PDB. (-j option) cm_blast_iteration = 5 #evalue threshold of including into profile on PDB (-h option) #in old version: we didn't set this value. defalut is 0.001? #cm_including_evalue = 0.001 #this is the same as default. cm_including_evalue = 0.002 ##############################End of PDB blasting option################# #############################NR profile building option################### #number of iterations of blasting on NR for profile building. (-j option) nr_iteration_num = 3 #evalue threshold for returning from blasting on NR database #and is is also the initial blast evalue (psi-blast default is 1.0)(-e option) nr_return_evalue = 0.1 #evalue threshold for including in profile building on NR database (-h option) #old value (and still used by SSpro, FR feature generation is 1e-10, too small?) #nr_including_evalue = 0.001 #this is used in sspro, better? #nr_including_evalue = 0.0000000001 #nr_including_evalue = 0.001 #nr_including_evalue = 0.0000000001 nr_including_evalue = 0.0001 ###############################End of NR profile building options######### #############################Alignment Combination Options############## #maximum allowed gap for stopping the alignment generation #cm_max_gap_size = 20 #cm_max_gap_size = 15 cm_max_gap_size = -1 #minimum covered size for one template to be chosen #cm_min_cover_size = 20 cm_min_cover_size = 15 #Modeller Option #From blast comparative modeling, how many #models to simulate. One model with lowest energy will be chosen. #cm_model_num = 10 cm_model_num = 10 #number of models to predict easy_model_num=5 #model prefix name output_prefix_name=hmmer #set the combination method #1. blast_comb (first version of simple combination). #if set to this option, cm_align_blast.pl will be used. #2. new_comb (latest version of alignment combination) #if set to this option, blast_align_comb.pl will be used. cm_comb_method=new_comb #cm_comb_method=blast_comb #option for advanced combination only (new_comb && cm_max_liner_size>=0) #<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=5 #option to use simple/advanced combination #>=0: use advanced combination. value is the max linker size at two ends #<0: use simple combination #must be an integer cm_max_linker_size=10 #threshold to include significant matched templates #templates with evalue lower than e^value will always #be included no matter how many gaps are filled by this alignment. #for negative number: the real evalue is: 1e^num (always positive) #for 0: means only combined if it can cover gaps disregard significance. #for 0: don't simply combine significant templates with low evalues #for negative number: real value = 1*10^cm_evalue_comb #for positive number: real value = cm_evalue_comb * 10^-0 #cm_evalue_comb=0 cm_evalue_comb=-20 #option to decide if the redundant alignments should be removed #yes: remove, no: not remove cm_clean_redundant_align=no #for the unconditional evalue combination, this option control the evalue difference #threshold of adding a less significant templates #e.g., 10: means the evalue exponent difference must be less than 10 cm_evalue_diff=10 #########################End of Alignment Combination Options################# ##########################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_blast_align=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_blast_local_ratio=2 #ratio of resolution difference for being considered exchange. #in Angstrom. #only valid if sort_blast_align is set to yes. sort_blast_local_delta_resolution=2 #Option for adding stx information and remove identical by resolution #yes: do it. no: don't. add_stx_info_rm_identical=no #resolution difference that decide if the redundant alignment will #be removed. bigger, more strict. rm_identical_resolution=2 ###############################End of sorting and stx information option#######