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AutoModel reference
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MODELLER A Program for
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Changes since release 10.3
Contents
Index
Comparative modeling class reference
Subsections
AutoModel
reference
AutoModel() — prepare to build one or more comparative models
AutoModel.library_schedule — select optimization schedule
AutoModel.md_level — control the model refinement level
AutoModel.outputs — all output data for generated models
AutoModel.rand_method — control initial model randomization
AutoModel.generate_method — control initial model generation
AutoModel.max_var_iterations — select length of optimizations
AutoModel.repeat_optimization — number of times to repeat optimization
AutoModel.max_molpdf — objective function cutoff
AutoModel.initial_malign3d — initial template alignment
AutoModel.starting_model — first model to build
AutoModel.ending_model — last model to build
AutoModel.final_malign3d — final template-model alignment
AutoModel.write_intermediates — write intermediate files during optimization
AutoModel.trace_output — control optimization output
AutoModel.max_ca_ca_distance — Distance cutoff for CA-CA homology-derived restraints
AutoModel.max_n_o_distance — Distance cutoff for N-O homology-derived restraints
AutoModel.max_sc_mc_distance — Distance cutoff for sidechain-mainchain homology-derived restraints
AutoModel.max_sc_sc_distance — Distance cutoff for sidechain-sidechain homology-derived restraints
AutoModel.blank_single_chain — Control chain ID for single-chain models
AutoModel.set_output_model_format() — set format for output models
AutoModel.get_optimize_actions() — get actions to carry out during the initial optimization
AutoModel.get_refine_actions() — get actions to carry out during the refinement
AutoModel.select_atoms() — select region for optimization and assessment
AutoModel.auto_align() — generate an automatic initial alignment
AutoModel.very_fast() — request rapid optimization
AutoModel.make() — build all models
AutoModel.cluster() — cluster all built models
AutoModel.special_restraints() — add additional restraints
AutoModel.nonstd_restraints() — add restraints on ligands
AutoModel.special_patches() — add additional patches to the topology
AutoModel.user_after_single_model() — analyze or refine each model
AutoModel.get_model_filename() — get the model PDB/mmCIF name
AutoModel.use_parallel_job() — parallelize model building
AutoModel.guess_atom_types() — automatically assign C
HARMM
atom types
AutoModel.guess_atom_type() — automatically assign C
HARMM
atom type
AllHModel
reference
AllHModel() — prepare to build all-hydrogen models
LoopModel
reference
LoopModel() — prepare to build models with loop refinement
LoopModel.loop.md_level — control the loop model refinement level
LoopModel.loop.max_var_iterations — select length of optimizations
LoopModel.loop.library_schedule — select optimization schedule
LoopModel.loop.starting_model — first loop model to build
LoopModel.loop.ending_model — last loop model to build
LoopModel.loop.write_selection_only — write PDB/mmCIFs containing only the loops
LoopModel.loop.write_defined_only — only write non-loop atoms present in the input model
LoopModel.loop.outputs — all output data for generated loop models
LoopModel.select_loop_atoms() — select region for loop optimization and assessment
LoopModel.get_loop_model_filename() — get the model PDB/mmCIF name
LoopModel.user_after_single_loop_model() — analyze or refine each loop model
LoopModel.read_potential() — read in the loop modeling potential
LoopModel.build_ini_loop() — create the initial conformation of the loop
DOPELoopModel
reference
DOPELoopModel() — prepare to build models with DOPE loop refinement
DOPEHRLoopModel
reference
