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automodel reference
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MODELLER A Program for
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Changes since release 9.22
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
dope_loopmodel
reference
dope_loopmodel() — prepare to build models with DOPE loop refinement
dopehr_loopmodel
reference
