======================================== === Build the ARP2/3 complex ==== ======================================== =====0. user preparation The user needs to prepare: I. a file with the subunits list. Each line describes a subunit and contains: name pdb_file num_copies. (1tyq.subuits) Make sure that the subunit names are unique. II. a mrc file of the assembly (input/1tyq_15.mrc) =====1.generate the parameters file multifit.py param -i 1tyq.asmb.input -- 1tyq input/1tyq.subunit.list.txt 15 input/1tyq_10.mrc 10 3.3 0.28 -99.375000 -62.513000 -40.181999 The parameters are: 1tyq.subunits : list of subunits 15 : coarsening level, 15 residues per bead is recommeted input/1tyq_10.mrc : the density map 10 : the resolution 3.3 : the spacing 155 : the threshold -83.6 -46.2 -24.2 : the origin -i 1tyq.asmb.input : the name of the assembly input file A file named 1tyq.asmb.input is generated. This file holds all parameters required for the MultiFit stages In addition, a filed named 1tyq.alignment.param is generated for step 5. =====2. Running MultiFit The steps to execute: ==2.1 generate the assembly anchor graph multifit.py anchors 1tyq.asmb.input 1tyq.asmb.anchors Files being generated: 1tyq.asmb.anchors.pdb : The graph in pdb format 1tyq.asmb.anchors.txt : The graph in txt format 1tyq.asmb.anchors.cmm : The graph in cmm format ==2.2 generate the fits multifit.py fit_fft -c 6 1tyq.asmb.input -n 1000 (for benchmarking; if names of PDBs in native orientation are added to the rightmost column in 1tyq.asmb.input, the RMSD of each fit to native can be generated by running multifit.py add_fit_rmsd 1tyq.asmb.input ) ==2.3 generate indexes multifit.py indexes 1tyq 1tyq.asmb.input 1000 1tyq.indexes.mapping.input ==2.4 create a proteomics file multifit.py proteomics 1tyq.asmb.input 1tyq.asmb.anchors.txt 1tyq.proteomics.input Anchor combinations based on the fits are generated ==2.5 assemble fitting solutions multifit.py align 1tyq.asmb.input 1tyq.proteomics.input 1tyq.indexes.mapping.input 1tyq.alignment.param 1tyq.combinations.output 1tyq.scores.output ==2.6 Write individual solutions to write out all solutions call: multifit.py models 1tyq.asmb.input 1tyq.combinations.output 1tyq.asmb.mdl It will write the solutions as: 1tyq.asmb.mdl.001.pdb .... ==2.7. For debugging, if the reference structures are added to the 1tyq.asmb.input file, you can get the rmsds using: multifit.py rmsd 1tyq.asmb.input 1tyq.proteomics.input 1tyq.indexes.mapping.input 1tyq.combinations.output 1tyq.combinations.rmsd.output ====3. Refine the first model ==3.0 create the first model and split it into chains >>$IMP/tools/imppy.sh python $IMP/modules/multifit2/bin/write_ensemble_models.py -m 1 1tyq.asmb.input 1tyq.combinations.output 1tyq.asmb.mdl multifit.py split 1tyq.asmb.mdl.0.pdb >> manually create 1tyq.subunit.refined.list.txt ==3.1 create the parameters file $IMP/tools/imppy.sh python $IMP/modules/multifit2/bin/generate_assembly_input.py -i 1tyq.asmb.refined.input -- 1tyq 1tyq.subunit.refined.list.txt 15 input/1tyq_10.mrc 10 3.3 0.28 -99.375000 -62.513000 -40.181999 ==3.3 generate the fits $IMP/tools/imppy.sh python $IMP/modules/multifit2/bin/run_fitting_fft.py -c 6 1tyq.asmb.refined.input 1tyq.subunit.refined.list.txt [[ debugging command, get the RMSD of each fit $IMP_NEW_FAST/tools/imppy.sh python $IMP_NEW_SRC/modules/multifit/pyext/src/add_rmsd_column_for_fitting_solutions.py 1tyq.asmb.input 1tyq.proteomics.input 1tyq.indexes.mapping.input 1tyq.alignment.param ]] ==3.4 generate indexes $IMP/tools/imppy.sh python $IMP/modules/multifit2/bin/generate_indexes_from_fitting_solutions.py 1tyq.refined 1tyq.asmb.refined.input 100 ==3.5 create proteomics file $IMP/tools/imppy.sh python multifit.py proteomics 1tyq.asmb.input 1tyq.asmb.anchors.txt 1tyq.proteomics.input ==3.6 assmble $IMP/tools/imppy.sh python $IMP/modules/multifit/pyext/src/align.py 1tyq.asmb.refined.input 1tyq.refined.proteomics.input 1tyq.refined.indexes.mapping.input 1tyq.alignment.param 1tyq.docking.param 1tyq.refined.combinations.output 1tyq.refined.scores.output ===== Extra things, to be validated: Valid combinations of fits are generated ==2.5 analyse the ensemble $IMP/tools/imppy.sh python $IMP/modules/multifit2/bin/ensemble_analysis.py 1tyq.asmb.input paths.output ==2.5. write the output $IMP/tools/imppy.sh python $IMP/modules/multifit2/bin/create_output_file.py asmb.input paths.output Solutions are scored. The output is written to : multifit.output, each line is of the format for a 4 protein complex: solution index | solution filename | fitting score| ev score | prot1 transformation |prot2 transformation |prot3 transformation |prot4 transformation | == 2.6 create all docking solutions $IMP/tools/imppy.sh python ../bin/run_pairwise_docking.py asmb.input #convering to IMP format ==2.7 [for debugging calculate the RMSD of the docking solutions] ===== TO ADD, not fully supported at this point 8. improve by pairwise docking $IMP/tools/imppy.sh python $IMP/modules/multifit2/bin/assemble_paths.py asmb.input 9. minimize ================================ == 1. Create fine parameters $IMP/tools/imppy.sh python $IMP/modules/multifit2/bin/generate_assembly_input.py -i asmb.refined.input -- input/1tyq.subunit.list.txt 3 input/1tyq_15.mrc 15 2 300 30 4 -96 == 2. Create the fine anchors $IMP/tools/imppy.sh python $IMP/modules/multifit2/bin/generate_anchors.py asmb.refined.input ================================== ===== Rank by CC match $IMP/tools/imppy.sh python $IMP/modules/multifit2/bin/score_by_points_matching.py input/1tyq_A.pdb A_fitting_rmsd.txt 10 A_anchors.fine.txt em_anchors.FINE.txt A_fitting_rmsd_point_match_score.txt $IMP/tools/imppy.sh python $IMP/modules/multifit2/bin/score_by_points_matching.py input/1tyq_B.pdb B_fitting_rmsd.txt 10 B_anchors.fine.txt em_anchors.FINE.txt B_fitting_rmsd_point_match_score.txt $IMP/tools/imppy.sh python $IMP/modules/multifit2/bin/score_by_points_matching.py input/1tyq_C.pdb C_fitting_rmsd.txt 10 C_anchors.fine.txt em_anchors.FINE.txt C_fitting_rmsd_point_match_score.txt $IMP/tools/imppy.sh python $IMP/modules/multifit2/bin/score_by_points_matching.py input/1tyq_D.pdb D_fitting_rmsd.txt 10 D_anchors.fine.txt em_anchors.FINE.txt D_fitting_rmsd_point_match_score.txt