2DLattice

Program code used in the design of 2D lattices with de novo building blocks

Step 1. Rapid generation of connecting and non-clashing 2D lattices from protein building blocks

~/Rosetta/main/source/bin/flatland.static.linuxgccrelease
-in:file:s [input pdb model]
-database [path to Rosetta database]
-ignore_unrecognized_res
-mh:path:scores_BB_BB /gscratch/baker/zibochen/utilities/aa_count_ACDEFHIKLMNQRSTVWY_resl1_ang15_msc0.2_smooth1.3_ROSETTA/aa_count_ACDEFHIKLMNQRSTVWY_resl1_ang15_msc0.2_smooth1.3_ROSETTA -mh:score:use_ss1 true -mh:score:use_ss2 true -mh:score:use_aa1 false -mh:score:use_aa2 false #motif score specific options
-symmetry_definition dummy
-output_virtual
-tag [user defined name tag for the job]
-rot_step [search step size for the self-rotation of the building block, takes a real number]
-Cn [internal cyclic symmetry of the building block, 2]
-wallpaper [layer symmetry of the final 2D lattice, C211]
-dump_silent [dump a silent file containing all the lattices, boolean]
-C211_B [lattice parameter B for the C 1 2 layer group, takes a real number]
-cell_upper [upper limit for the cell dimensions, takes a real number]
-single_chain_version [if the input model is monomerized, the code accomondates for this psudeo-symmetry. Boolean]
-cell_step [search step size for the lattice cell dimensions, takes a real number]

Step 2. HBNet search at the interfaces of extracted adjacent building blocks

~/Rosetta/main/source/bin/rosetta_scripts.static.linuxgccrelease
-in:file:s [input pdb model]
-out::file::pdb_comments
-run:preserve_header
-use_input_sc
-out:prefix HBNet_
-beta
-missing_density_to_jump true
-parser:protocol 2D_HBNet.xml
-database [path to Rosetta database]
-chemical:exclude_patches LowerDNA UpperDNA Cterm_amidation VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phos phorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm
-in:file:fullatom
-multi_cool_annealer 10
-no_optH false
-optH_MCA true
-flip_HNQ

Step 3. Regenerate the complete 2D lattice and map newly designed interfaces to all symmetric copies

~/Rosetta/main/source/bin/symm_seq_gen_2D.default.linuxgccrelease
-database [path to Rosetta database]
-s [input pdb model]
-cn [symmetry of the building block, 2]

Step 4. Symmetric design of the 2D lattice in the context of its symmetry

~/Rosetta/main/source/bin/symm_seq_gen_2D.default.linuxgccrelease
-database [path to Rosetta database] \ -in:file:silent [input Rosetta silent file containing the 2D lattice]
-parser:script_vars resfile=[input resfile to enfore newly designed interfaces stay intact]
-out::file::pdb_comments
-run:preserve_header
-multi_cool_annealer 10
-use_input_sc
-symmetry_definition dummy
-out:prefix packed_
-beta -missing_density_to_jump true
-symmetry:detect_bonds false
-parser:protocol 2D_final_design.xml