CHESS2FLYA 1.0 Thomas Aeschbacher & Markus Blatter 2013 ETH Zurich -------------------------------------------------------------------- The program CHESS2FLYA uses as input a file with secondary structure information in the .ct file format. This can be created manually or e.g. on "www.rnasoft.ca". chess2flya creates then a .prot file containing chemical shift prediction of all nucleotides of RNAs. Additionally an angle restraint file (.aco file), a sequence file (.seq file) are prepared. These files are then used as an input for FLYA automated assignment algorithm within CYANA (P.Guntert). chess2flya requires the statistics file Statfile.tab. Usage: chess2flya [options] ###################################################################################################### -h help -c prediction interval defined by the percentage of resonances in it [1-11] (default 2) 1: 50%, 2: 60%, 3: 70%, 4: 80, 5: 90%, 6: 95% 7: 98%, 8: 99%, 9: 99.5%, 10: 99.8%, 11: 99.9% -f file with statistics table (default Statfile.tab) -s file with RNA sequence and secondary structure (default rnass.ct) The file has to be in the .ct format and can be created e.g. on http://www.rnasoft.ca/ . ###################################################################################################### ./chess2flya -h #--> Help appears ./chess2flya #--> Creates 60% prediction itervals for each shift of the secondary structure file 'rnass.ct' (Standard input file) ./chess2flya -s 'input.ct' #--> Creates 60% prediction itervals for each shift of the secondary structure file 'input.ct' ./chess2flya -s 'input.ct' -c 3 #--> Creates 70% prediction itervals for each shift of the secondary structure file 'input.ct' ####################### # Given example: # RNA stemloop FZL4 ####################### cd CHESS2FLYA/demo ../chess2flya -s FZL4.ct -f ../Statfile.tab #--> generates: cyana.aco, cyana.prot, cyana.seq, cyana.wc ############################################################################################# #----------------------------------FLYA----(Peter Guntert)----------------------------------# ############################################################################################# # requires Cyana3.9 setup cyana39 #nothing else works # Unpack the FLYA.tar file by tar -xvf FLYA.tar # FLYA uses two directories, one with the original input data ("orig"), one for the # actual calculation with the name of the project ("FZL4") # "orig" should be accessible from "FZL4" via "../orig" mkdir FZL4 #--> already created from the tar file mkdir orig #--> already created from the tar file #required files in these direcctories: # peak lists of the 1H-13C HSQC, 2D TOCSY and 2D NOESY spectra and for comparison also # the assigned shift lists (if available) in xeasy format ./orig/FZL4_HSQC_PeakList #--> if a 13C(aro) and a 13C(ali) HSQC was measured both peak lists have to be combined to one ./orig/FZL4_NOESY_PeakList ./orig/FZL4_TOCSY_PeakList ./orig/FZL4_HSQC_ShiftList ./orig/FZL4_NOESY_ShiftList ./orig/FZL4_TOCSY_ShiftList ./orig/FZL4.aco #--> from cp ./CHESS2FLYA/cyana.aco ./orig/FZL4.aco ./orig/FZL4.prot #--> from cp ./CHESS2FLYA/cyana.prot ./orig/FZL4.prot ./orig/FZL4.wc #--> from cp ./CHESS2FLYA/cyana.wc ./orig/FZL4.wc # CYANA run macros ./FZL4/PREP.cya #--> please see the content of PREP.cya at the end ./FZL4/init.cya #--> please see the content of init.cya at the end ./FZL4/FLYA.cya #--> please see the content of FLYA.cya at the end ./FZL4/FZL4.seq #--> from cp ./CHESS2FLYA/cyana.seq ./orig/FZL4.seq # in FZL4 directory: # source CYANA 3.9 (or later) executables and run PREP.cya followed by FLYA.cya cyana PREP.cya --> this will generate the following files: stat.prot ref.prot NOESY.peaks TOCSY.peaks C13H1.peaks all.aco cyana FLYA.cya --> this will generate the following files: flya.tab flya.prot TOCSY_exp.peaks TOCSY_asn.peaks NOESY_exp.peaks NOESY_asn.peaks C13H1_exp.peaks C13H1_asn.peaks flya.txt ########################################--PREP.cya--########################################## dir := ../orig input := FZL4_NOESY_PeakList,FZL4_TOCSY_PeakList,FZL4_HSQC_PeakList spectra := NOESY,TOCSY,C13H1 format := NOESY H1 H2, TOCSY H1 H2, C13H1 C H read prot $dir/FZL4.prot unknown=warn write prot stat.prot read prot $dir/FZL4_NOESY_ShiftList| unknown=warn read prot $dir/FZL4_TOCSY_ShiftList| unknown=warn add read prot $dir/FZL4_HSQC_ShiftList| unknown=warn add write prot ref.prot do i 1 length('spectra') read prot ref.prot read peaks $dir/$input(i)| format="$format(i)" write peaks $spectra(i) names end do read $dir/FZL4.aco unknown=warn write all.aco system "cp -a $dir/FZL4.wc wc.cya" ############################################################################################## ########################################--FLYA.cya--########################################## #noesy:=NOESY #scalar:=TOCSY,C13H1 calibration := # NOE calibration parameters structures := 500,20 # number of initial, final structures steps := 10000 # number of torsion angle dynamics steps upl_values := 2.4,5.2 randomseed := 57923 # random number generator seed run_assign_reference:=ref.prot run_assign_iterations:=15000 run_assign_population:=100 run_assign_statistics:=stat.prot analyze_assign_group:="SugarC: C1\' H1\' / CONSOLIDATED, BasesC: C2 H2 C5 H5 C6 H6 C8 H8 / CONSOLIDATED, StemC: 1..8 14..21 C2 H2 C5 H5 C6 H6 C8 H8 C1\' H1\' / CONSOLIDATED, AllC: CONSOLIDATED, Sugar: C1\' H1\', Bases: C2 H2 C5 H5 C6 H6 C8 H8, Stem: 1..8 14..21 C2 H2 C5 H5 C6 H6 C8 H8 C1\' H1\', ALL: *" if (.not.existfile('start.pdb')) then ./init read aco all.aco wc sugarbond calc_all 100 #vtfmin overview start.ovw structures=20 pdb end if flya refprot=ref.prot noesy=$noesy scalar=$scalar runs=50 plot= ############################################################################################## ########################################--init.cya--########################################## path:=.,$cyanadir/macro name:=FZL4 cyanalib read seq $name.seq noesy:=NOESY scalar:=TOCSY,C13H1 tolerance:=0.02,0.02,0.3 assigncs_accH:=tolerance(1) assigncs_accC:=tolerance(3) assigncs_accN:=tolerance(3) command NOESY_expect peaks atoms select "C1\' H1\' C2 H2 C5 H5 C6 H6 C8 H8 - C*" spectrum $peaks append distance=4.0 structures=20 probability=0.9 spectrum $peaks append distance=6.0 structures=20 probability=0.8 spectrum $peaks append distance=9.0 structures=20 probability=0.5 spectrum $peaks append distance=14.0 structures=20 probability=0.3 write # atom select "*" # spectrum $peaks append distance=6.0 structures=20 probability=0.01 end command TOCSY_expect peaks atoms select "H5 H6 URA RCYT" spectrum $peaks skipdiagonal append write end command C13H1_select atoms select "C1\' H1\' C2 H2 C5 H5 C6 H6 C8 H8" end ##############################################################################################