Print JOB "mv iam.running iam.failed \n " Print JOB "echo \"ERROR! Final structures not found! \" \n " Print JOB " echo \"accepted structures written. " residue not defined! \nFile: $chain! \nLine : $_ " if ( not defined $AA3TO1.pdb \" ] then \n "
Next unless (parse_pdb_row( $_, "aname ") eq "CA ") Ĭonfess "ERROR!: ".parse_pdb_row( $_, "rname "). My $sequence = substr $REFSEQUENCE, 0, $L My $REFSEQUENCE = "RSEDWQCPRTPYAASRDFDVKYVVPSFSAGGLVQAMVTYEGDRNESAVFVAIRNRLHVLGPDLKSVQSLATGPAGDPGCQTCAACGPGPHGPPGDTDTKVLVLDPALPALVSCGSSLQGRCFLHDLEPQGTAVHLAAPACLFSAHHNRPDDCPDCVASPLGTRVTVVEQGQASYFYVASSLDAAVAGSFSPRSVSIRRLKADASGFAPGFVALSVLPKHLVSYSIEYVHSFHTGAFVYFLTVQPASVTDDPSALHTRLARLSATEPELGDYRELVLDCRFAPKLVPRGSPEGGQPYPVLQVAHSAPVGAQLATELSIAEGQEVLFGVFVTGKDGGPGVGPNSVVCAFPIDLLDTLIDEGVERCCESPVHPGLRRGLDFFQSPSFCPNPPGLEALSPNTSCRHFPLLVSSSFSRVDLFNGLLGPVQVTALYVTRLDNVTVAHMGTMDGRILQVELVRSLNYLLYVSNFSLGDSGQPVQRDVSRLGDHLLFASGDQVFQVPIQGPGCRHFLTCGRCLRAWHFMGCGWCGNMCGQQKECPGSWQQDHCPPKLTEFHPHSGPLRGSTRLTLCGSNFYLHPSGLVPEGTHQVTVGQSPCRPLPKDSSKLRPVPRKDFVEEFECELEPLGTQAVGPTNVSLTVTNMPPGKHFRVDGTSVLRGFSFMETG "
IF2dist_new( " $ID.txt ", " $ID.dist ", $KSCALING)
#My j.a.r.v.i.s setup with michael c's jarvis program pro
Our %AA3TO1 = qw(ALA A ASN N CYS C GLN Q HIS H LEU L MET M PRO P THR T TYR Y ARG R ASP D GLU E GLY G ILE I LYS K PHE F SER S TRP W VAL V ) Ĭonfess "ERROR! Cannot find CNS suite folder at $cns_suite! Check CNS installation! " if not -d $cns_suite Ĭonfess "ERROR! cns_solve_env.sh not found inside $cns_suite/! Check CNS installation! " if not -f " $cns_suite/cns_solve_env.sh " Ĭonfess "ERROR! CNS executable $cns_executable not found! Check CNS installation! " if not -f $cns_executable Ĭonfess "ERROR! protein.param not found inside $cns_suite/libraries/toppar/! Check CNS installation! " if not -f " $cns_suite/libraries/toppar/protein.param " System_cmd( "cp $file_if $dir_out/ ") if not -f $ID Print "Effective Conversion Equation is : D = $KSCALING/ \n " Print_usage( "Output directory $dir_out does not exist! ") if not -d $dir_out Mkdir $dir_out or confess "ERROR! Could not create output directory $dir_out! " if not -d $dir_out $MODELCOUNT = 20 if not defined $MODELCOUNT Print_usage( "Input IF file $file_if does not exist! ") if not -f $file_if Print_usage( "Output directory not defined! ") if not defined $dir_out Print_usage( "Input IF matrix not found! ") if not defined $file_if Or confess "ERROR! Error in command line arguments! " My $dg_sa_log = "/dev/null " # replace with dgsa.log if space is NOT a concern My $cns_executable = " $cns_suite/intel-x86_64bit-linux/bin/cns_solve " My $cns_suite = "/home/bap54/chr3D_projects/project01/programs/cns_solve_1.3 "
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