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automodel reference
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MODELLER A Program for
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Loop optimization
Contents
Index
Comparative modeling class reference
Subsections
automodel
reference
automodel() -- prepare to build one or more comparative models
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.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.special_patches() -- add additional patches to the topology
automodel.user_after_single_model() -- analyze or refine each model
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.starting_model -- first loop model to build
loopmodel.loop.ending_model -- last loop model to build
loopmodel.loop.outputs -- all output data for generated loop models
loopmodel.select_loop_atoms() -- select region for loop optimization
Ben Webb 2006-02-28
