| Filename |
Description |
| __ model.top |
the main script for comparative modeling with user alignment |
| __ full_homol.top |
the main script for comparative modeling with automatic alignment |
| __ loop.top |
loop modeling |
| __ defs.top |
variable definitions for modeling by model |
| __ align_strs_seq.top |
aligning many structures with a sequence |
| __ getnames.top |
generating default filenames from protein codes |
| __ homcsr.top |
generating homology-derived restraints |
| __ spline.top |
generating splined restraints |
| __ cispeptide.top |
defining cis-peptides |
| __ default_patches.top |
making topology patches during modeling by model |
| __ special.top |
generating and reading special restraints/patches for modeling by model |
| __ generate_model.top |
generating initial models for modeling by model |
| __ single_model.top |
used by model to generate a single model |
| __ multiple_models.top |
used by model to generate an ensemble of models |
| __ refine.top |
molecular dynamics refinement for modeling by model |
| __ loop.top |
modeling of loops |
| __ principal.top |
principal components clustering |
| __ cluster.top |
optimization by 'clustering' and refinement |
| __ spline. top |
spline most restraint types in memory |
| __ asgl_mod.top |
plotting for clustering analysis (requires ASGL) |
| __ complete.top |
generating missing atoms in a PDB file |
| __ fit.top |
superposing two structures, given an alignment |
| __ mod.top |
the main include file including all other __*.top files |
