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automodel reference
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MODELLER A Program for
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Changes since release 9.11
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.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
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 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 PDBs 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
loopmodel.get_loop_model_filename() -- get the model PDB 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
Automatic builds 2014-02-11
