ROSETTA
A python script in order to search popular clusters from the outputs of clustering analysis in Rosetta.
import re
import math
import os
File = open('list.dat', 'r')
os.system("ls *.pdb > list.dat")
l = []
for line in File:
d= re.split('(?<!\d)[,.]|[,.](?!\d)', line)
f = float(d[1])
v = math.modf(f)
d = v[0]
e = len(str(d))
if e ==3:
h =d*10
l.append(h)
else:
q = d*100
l.append(q)
M = (max(l))
os.system("ls c.*.%g.pdb.pdb" %(M))
Input file for prediction of protein structures using Abinitio approach.
source /RS/progs/rosetta/3.4_gcc_openmpi/ENVARS
mpirun.lsf /RS/progs/rosetta/3.4_gcc_openmpi/bin/AbinitioRelax.mpi.linuxgccrelease \
-database /RS/progs/rosetta/3.4_database \
-in:file:fasta cyto.fasta \
-in:file:frag3 aat000_03_05.200_v1_3 \
-in:file:frag9 aat000_09_05.200_v1_3 \
-abinitio:relax \
-relax:fast \
-abinitio::increase_cycles 10 \
-abinitio::rg_reweight 0.5 \
-abinitio::rsd_wt_helix 0.5 \
-abinitio::rsd_wt_loop 0.5 \
-use_filters true \
-out:file:silent FKRP_silent.out \
-constant_seed \
-jran 1234567 \
-seed_offset 10 \
-nstruct 20000
Input file for clustering analysis in Rosetta.
source /RS/progs/rosetta/3.5_gcc_openmpi/ENVARS
mpirun.lsf /RS/progs/rosetta/3.5_gcc_openmpi/bin/cluster.linuxgccrelease \
-database /RS/progs/rosetta/3.5_database \
-in:file:silent ../FKRP_silent_*.out \
-in:file:fullatom \
-out:file:silent FKRP-cluster.out \
-run:shuffle \
-cluster:radius -1 \
>&cluster.log
#Script for (re)modelling of the loops
/loopmodel.default.linuxgccrelease \
-database /rosetta_database \
-nstruct 1000 #at least
-loops:input_pdb ../crystal.pdb \
-loops:loop_file ../input.loop \
-loops:remodel perturb_kic \
-loops:refine refine_kic \
-loops.max_kic_build_attempts 100 \
-loops:fix_natsc true \
-loops:neighbor_dist 0.0 \
-loops:relax fastrelax \
-loops:extended \
-ex1 \
-ex2 \
-out:path:pdb ./ \
-out:suffix $i \
-out:file:fullatom \
-out:pdb \
#Script for flexible protein-protein docking
#Step 1
#!/bin/bash
/home/ramin/Downloads/rosetta_2014wk05_bundle/main/source/bin/FlexPepDocking.mpi.linuxgccrelease \
-database /home/ramin/Downloads/rosetta_2014wk05_bundle/main/database \
-s closed-bekm1.pdb \
-native closed-bekm1.pdb \
-receptor_chain A \
-peptide_chain B \
-flexpep_prepack \
-ex1 \
-ex2aro \
#Step 2
#!/bin/bash
mpirun -np 6 /home/ramin/Downloads/rosetta_2014wk05_bundle/main/source/bin/FlexPepDocking.mpi.linuxgccrelease \
-database /home/ramin/Downloads/rosetta_2014wk05_bundle/main/database \
-s closed-bekm1-pre.pdb \
-receptor_chain A \
-peptide_chain B \
-out:file:silent decoys.silent \
-out:file:silent_struct_type binary \
-pep_refine \
-ex1 \
-ex2aro \
-native closed-bekm1-pre.pdb \
-use_input_sc \
-nstruct 20 \
-lowres_preoptimize \