<p>MODELLER </p><p>A Program for Protein Structure Modeling <br>Release 10.1, r12156 </p><p>ˇ<br>Andrej Sali </p><p>with help from <br>Ben Webb, M.S. Madhusudhan, Min-Yi Shen, Guangqiang Dong, Marc A. Martı-Renom, Narayanan Eswar, Frank Alber, Maya Topf, Baldomero Oliva, Andr´as Fiser, Roberto S´anchez, Bozidar Yerkovich, <br>Azat Badretdinov, Francisco Melo, John P. Overington, and Eric Feyfant </p><p>email: modeller-care AT salilab.org URL <a href="/goto?url=https://salilab.org/modeller/" target="_blank">https://salilab.org/modeller/ </a></p><p>2021/03/12 </p><p>ii </p><p>Contents </p><p>Copyright notice Acknowledgments xxi xxv </p><ul style="display: flex;"><li style="flex:1">1</li><li style="flex:1">Introduction </li><li style="flex:1">1</li></ul><p></p><p>12345889<br>1.1 What&nbsp;is Modeller? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.2 Modeller bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.3 Obtaining&nbsp;and installing the program .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.4 Bug&nbsp;reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.5 Method&nbsp;for comparative protein structure modeling by Modeller . . . . . . . . . . . . . . . . . . . 1.6 Using&nbsp;Modeller for comparative modeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . <br>1.6.1 Preparing&nbsp;input files&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.6.2 Running&nbsp;Modeller . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . </p><p></p><ul style="display: flex;"><li style="flex:1">2</li><li style="flex:1">Automated comparative modeling with AutoModel </li><li style="flex:1">11 </li></ul><p></p><p>2.1 Simple&nbsp;usage .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;11 2.2 More&nbsp;advanced usage .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;12 <br>2.2.1 Including&nbsp;water molecules, HETATM residues, and hydrogen atoms&nbsp;. . . . . . . . . . . . . .&nbsp;12 2.2.2 Changing&nbsp;the default optimization and refinement protocol&nbsp;. . . . . . . . . . . . . . . . . . .&nbsp;14 2.2.3 Getting&nbsp;a very fast and approximate model&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;14 2.2.4 Building&nbsp;a model from multiple templates&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;15 2.2.5 Building&nbsp;an all hydrogen model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;16 2.2.6 Refining&nbsp;only part of the model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;16 2.2.7 Including&nbsp;disulfide bridges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;18 2.2.8 Generating&nbsp;new-style PDBx/mmCIF outputs&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;19 2.2.9 Providing&nbsp;your own restraints file .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;19 2.2.10 Using&nbsp;your own initial model&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;20 2.2.11 Adding&nbsp;additional restraints to the defaults&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;21 2.2.12 Building&nbsp;multi-chain models .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;22 2.2.13 Residues&nbsp;and chains in multi-chain models .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;23 2.2.14 Accessing&nbsp;output data after modeling is complete .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . .&nbsp;24 2.2.15 Fully&nbsp;automated alignment and modeling&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;25 <br>2.3 Loop&nbsp;optimization .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;26 <br>2.3.1 Automatic&nbsp;loop refinement after model building .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;26 2.3.2 Defining&nbsp;loop regions for refinement&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;27 iv </p><p>CONTENTS </p><p>2.3.3 Refining&nbsp;an existing PDB file&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;28 </p><p></p><ul style="display: flex;"><li style="flex:1">3</li><li style="flex:1">Frequently asked questions and history </li><li style="flex:1">31 </li></ul><p></p><p>3.1 Frequently&nbsp;asked questions (FAQ) and examples&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;31 3.2 Modeller updates .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;38 <br>3.2.1 Changes&nbsp;since release 10.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;38 3.2.2 Changes&nbsp;since release 9.25 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;38 </p><p></p><ul style="display: flex;"><li style="flex:1">4</li><li style="flex:1">Comparative modeling class reference </li><li style="flex:1">39 </li></ul><p></p><p>4.1 AutoModel reference .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;39 <br>4.1.1 AutoModel()&nbsp;— prepare to build one or more comparative models&nbsp;. . . . . . . . . . . . . . .&nbsp;39 4.1.2 AutoModel.library&nbsp;schedule — select optimization schedule&nbsp;. . . . . . . . . . . . . . . . . . .&nbsp;40 4.1.3 AutoModel.md&nbsp;level — control the model refinement level .&nbsp;. . . . . . . . . . . . . . . . . . .&nbsp;40 4.1.4 AutoModel.outputs&nbsp;— all output data for generated models .&nbsp;. . . . . . . . . . . . . . . . . .&nbsp;40 4.1.5 AutoModel.rand&nbsp;method — control initial model randomization&nbsp;. . . . . . . . . . . . . . . .&nbsp;40 4.1.6 AutoModel.generate&nbsp;method — control initial model generation .&nbsp;. . . . . . . . . . . . . . . .&nbsp;40 4.1.7 AutoModel.max&nbsp;var iterations — select length of optimizations&nbsp;. . . . . . . . . . . . . . . . .&nbsp;41 4.1.8 AutoModel.repeat&nbsp;optimization — number of times to repeat optimization&nbsp;. . . . . . . . . .&nbsp;41 4.1.9 AutoModel.max&nbsp;molpdf — objective function cutoff&nbsp;. . . . . . . . . . . . . . . . . . . . . . .&nbsp;41 4.1.10 AutoModel.initial&nbsp;malign3d — initial template alignment&nbsp;. . . . . . . . . . . . . . . . . . . .&nbsp;41 4.1.11 AutoModel.starting&nbsp;model — first model to build .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . .&nbsp;41 4.1.12 AutoModel.ending&nbsp;model — last model to build&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;41 4.1.13 AutoModel.final&nbsp;malign3d — final template-model alignment&nbsp;. . . . . . . . . . . . . . . . . .&nbsp;41 4.1.14 AutoModel.write&nbsp;intermediates — write intermediate files during optimization&nbsp;. . . . . . . .&nbsp;41 4.1.15 AutoModel.trace&nbsp;output — control optimization output&nbsp;. . . . . . . . . . . . . . . . . . . . .&nbsp;41 4.1.16 AutoModel.max&nbsp;ca ca distance — Distance cutoff for CA-CA homology-derived restraints . .&nbsp;42 4.1.17 AutoModel.max&nbsp;n o distance — Distance cutoff for N-O homology-derived restraints .&nbsp;. . . .&nbsp;42 4.1.18 AutoModel.max&nbsp;sc mc distance — Distance cutoff for sidechain-mainchain homology-derived restraints&nbsp;42 4.1.19 AutoModel.max&nbsp;sc sc distance — Distance cutoff for sidechain-sidechain homology-derived restraints&nbsp;42 4.1.20 AutoModel.blank&nbsp;single chain — Control chain ID for single-chain models . . . . . . . . . . .&nbsp;42 4.1.21 AutoModel.set&nbsp;output model format() — set format for output models .&nbsp;. . . . . . . . . . . .&nbsp;42 4.1.22 AutoModel.get&nbsp;optimize actions() — get actions to carry out during the initial optimization .&nbsp;43 4.1.23 AutoModel.get&nbsp;refine actions() — get actions to carry out during the refinement&nbsp;. . . . . . .&nbsp;43 4.1.24 AutoModel.select&nbsp;atoms() — select region for optimization and assessment&nbsp;. . . . . . . . . .&nbsp;43 4.1.25 AutoModel.auto&nbsp;align() — generate an automatic initial alignment . . . . . . . . . . . . . . .&nbsp;43 4.1.26 AutoModel.very&nbsp;fast() — request rapid optimization&nbsp;. . . . . . . . . . . . . . . . . . . . . . .&nbsp;43 4.1.27 AutoModel.make()&nbsp;— build all models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;43 4.1.28 AutoModel.cluster()&nbsp;— cluster all built models&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;44 4.1.29 AutoModel.special&nbsp;restraints() — add additional restraints&nbsp;. . . . . . . . . . . . . . . . . . .&nbsp;44 4.1.30 AutoModel.nonstd&nbsp;restraints() — add restraints on ligands&nbsp;. . . . . . . . . . . . . . . . . . .&nbsp;44 4.1.31 AutoModel.special&nbsp;patches() — add additional patches to the topology&nbsp;. . . . . . . . . . . .&nbsp;44 4.1.32 AutoModel.user&nbsp;after single model() — analyze or refine each model&nbsp;. . . . . . . . . . . . . .&nbsp;45 4.1.33 AutoModel.get&nbsp;model filename() — get the model PDB/mmCIF name .&nbsp;. . . . . . . . . . . .&nbsp;45 4.1.34 AutoModel.use&nbsp;parallel job() — parallelize model building .&nbsp;. . . . . . . . . . . . . . . . . . .&nbsp;45 </p><p>CONTENTS </p><p>v<br>4.1.35 AutoModel.guess&nbsp;atom types() — automatically assign Charmm atom types&nbsp;. . . . . . . . .&nbsp;45 4.1.36 AutoModel.guess&nbsp;atom type() — automatically assign Charmm atom type&nbsp;. . . . . . . . . .&nbsp;45 <br>4.2 AllHModel reference .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;46 <br>4.2.1 AllHModel()&nbsp;— prepare to build all-hydrogen models&nbsp;. . . . . . . . . . . . . . . . . . . . . .&nbsp;46 <br>4.3 LoopModel reference .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;46 <br>4.3.1 LoopModel()&nbsp;— prepare to build models with loop refinement .&nbsp;. . . . . . . . . . . . . . . . .&nbsp;46 4.3.2 LoopModel.loop.md&nbsp;level — control the loop model refinement level&nbsp;. . . . . . . . . . . . . .&nbsp;46 4.3.3 LoopModel.loop.max&nbsp;var iterations — select length of optimizations&nbsp;. . . . . . . . . . . . . .&nbsp;46 4.3.4 LoopModel.loop.library&nbsp;schedule — select optimization schedule&nbsp;. . . . . . . . . . . . . . . .&nbsp;47 4.3.5 LoopModel.loop.starting&nbsp;model — first loop model to build&nbsp;. . . . . . . . . . . . . . . . . . .&nbsp;47 4.3.6 LoopModel.loop.ending&nbsp;model — last loop model to build&nbsp;. . . . . . . . . . . . . . . . . . . .&nbsp;47 4.3.7 LoopModel.loop.write&nbsp;selection only — write PDB/mmCIFs containing only the loops .&nbsp;. . .&nbsp;47 4.3.8 LoopModel.loop.write&nbsp;defined only — only write non-loop atoms present in the input model&nbsp;47 4.3.9 LoopModel.loop.outputs&nbsp;— all output data for generated loop models&nbsp;. . . . . . . . . . . . .&nbsp;47 4.3.10 LoopModel.select&nbsp;loop atoms() — select region for loop optimization and assessment .&nbsp;. . . .&nbsp;47 4.3.11 LoopModel.get&nbsp;loop model filename() — get the model PDB/mmCIF name . . . . . . . . . .&nbsp;48 4.3.12 LoopModel.user&nbsp;after single loop model() — analyze or refine each loop model&nbsp;. . . . . . . .&nbsp;48 4.3.13 LoopModel.read&nbsp;potential() — read in the loop modeling potential&nbsp;. . . . . . . . . . . . . . .&nbsp;48 4.3.14 LoopModel.build&nbsp;ini loop() — create the initial conformation of the loop&nbsp;. . . . . . . . . . .&nbsp;48 <br>4.4 DOPELoopModel reference .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;48 <br>4.4.1 DOPELoopModel()&nbsp;— prepare to build models with DOPE loop refinement .&nbsp;. . . . . . . . .&nbsp;49 <br>4.5 DOPEHRLoopModel reference .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;49 </p><p></p><ul style="display: flex;"><li style="flex:1">5</li><li style="flex:1">Modeller general reference </li><li style="flex:1">51 </li></ul><p></p><p>5.1 Miscellaneous&nbsp;rules and features of Modeller . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;51 <br>5.1.1 Modeller system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;51 5.1.2 Controlling&nbsp;breakpoints and the amount of output&nbsp;. . . . . . . . . . . . . . . . . . . . . . . .&nbsp;51 5.1.3 File&nbsp;naming . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;51 5.1.4 File&nbsp;types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;53 <br>5.2 Stereochemical&nbsp;parameters and molecular topology&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;54 <br>5.2.1 Modeling&nbsp;residues with non-existing or incomplete entries in the topology and parameter libraries&nbsp;54 <br>5.3 Spatial&nbsp;restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;55 <br>5.3.1 Specification&nbsp;of restraints&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;55 5.3.2 Specification&nbsp;of pseudo atoms&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;58 5.3.3 Excluded&nbsp;pairs .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;59 5.3.4 Rigid&nbsp;bodies .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;60 5.3.5 Symmetry&nbsp;restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;61 </p><p></p><ul style="display: flex;"><li style="flex:1">6</li><li style="flex:1">Modeller command reference </li><li style="flex:1">65 </li></ul><p></p><p>6.1 Key&nbsp;for command descriptions&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;65 6.2 The&nbsp;Environ class: Modeller environment .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;65 <br>6.2.1 Environ()&nbsp;— create a new Modeller environment .&nbsp;. . . . . . . . . . . . . . . . . . . . . . .&nbsp;65 6.2.2 Environ.io&nbsp;— default input parameters .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;66 6.2.3 Environ.edat&nbsp;— default objective function parameters&nbsp;. . . . . . . . . . . . . . . . . . . . . .&nbsp;66 vi </p><p>CONTENTS </p><p>6.2.4 Environ.libs&nbsp;— Modeller libraries .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;66 6.2.5 Environ.schedule&nbsp;scale — energy function scaling factors .&nbsp;. . . . . . . . . . . . . . . . . . . .&nbsp;66 6.2.6 Environ.dendrogram()&nbsp;— clustering&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;66 6.2.7 Environ.principal&nbsp;components() — clustering&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;66 6.2.8 Environ.system()&nbsp;— execute system command&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;67 6.2.9 Environ.make&nbsp;pssmdb() — Create a database of PSSMs given a list of profiles&nbsp;. . . . . . . .&nbsp;67 <br>6.3 The&nbsp;EnergyData class: objective function parameters . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;69 <br>6.3.1 EnergyData()&nbsp;— create a new set of objective function parameters&nbsp;. . . . . . . . . . . . . . .&nbsp;69 6.3.2 EnergyData.contact&nbsp;shell — nonbond distance cutoff .&nbsp;. . . . . . . . . . . . . . . . . . . . . .&nbsp;69 6.3.3 EnergyData.update&nbsp;dynamic — nonbond recalculation threshold&nbsp;. . . . . . . . . . . . . . . .&nbsp;69 6.3.4 EnergyData.sphere&nbsp;stdv — soft-sphere standard deviation . . . . . . . . . . . . . . . . . . . .&nbsp;70 6.3.5 EnergyData.dynamic&nbsp;sphere — calculate soft-sphere overlap restraints&nbsp;. . . . . . . . . . . . .&nbsp;70 6.3.6 EnergyData.dynamic&nbsp;lennard — calculate Lennard-Jones restraints .&nbsp;. . . . . . . . . . . . . .&nbsp;70 6.3.7 EnergyData.dynamic&nbsp;coulomb — calculate Coulomb restraints&nbsp;. . . . . . . . . . . . . . . . .&nbsp;70 6.3.8 EnergyData.dynamic&nbsp;modeller — calculate non-bonded spline restraints&nbsp;. . . . . . . . . . . .&nbsp;70 6.3.9 EnergyData.excl&nbsp;local — exclude certain local pairs of atoms&nbsp;. . . . . . . . . . . . . . . . . .&nbsp;70 6.3.10 EnergyData.radii&nbsp;factor — scale atomic radii&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;70 6.3.11 EnergyData.lennard&nbsp;jones switch — Lennard-Jones switching parameters&nbsp;. . . . . . . . . . .&nbsp;70 6.3.12 EnergyData.coulomb&nbsp;switch — Coulomb switching parameters&nbsp;. . . . . . . . . . . . . . . . .&nbsp;71 6.3.13 EnergyData.relative&nbsp;dielectric — relative dielectric&nbsp;. . . . . . . . . . . . . . . . . . . . . . . .&nbsp;71 6.3.14 EnergyData.covalent&nbsp;cys — use disulfide bridges in residue distance&nbsp;. . . . . . . . . . . . . .&nbsp;71 6.3.15 EnergyData.nonbonded&nbsp;sel atoms — control interaction with picked atoms&nbsp;. . . . . . . . . .&nbsp;71 6.3.16 EnergyData.nlogn&nbsp;use — select non-bond list generation algorithm . . . . . . . . . . . . . . .&nbsp;71 6.3.17 EnergyData.max&nbsp;nlogn grid cells — maximum number of grid cells for NlogN nonbond pairs routine&nbsp;71 6.3.18 EnergyData.energy&nbsp;terms — user-defined global energy terms . . . . . . . . . . . . . . . . . .&nbsp;72 <br>6.4 The&nbsp;IOData class: coordinate file input parameters&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;73 <br>6.4.1 IOData()&nbsp;— create a new input parameters object&nbsp;. . . . . . . . . . . . . . . . . . . . . . . .&nbsp;73 6.4.2 IOData.hetatm&nbsp;— whether to read HETATM records&nbsp;. . . . . . . . . . . . . . . . . . . . . .&nbsp;73 6.4.3 IOData.hydrogen&nbsp;— whether to read hydrogen atoms&nbsp;. . . . . . . . . . . . . . . . . . . . . .&nbsp;73 6.4.4 IOData.water&nbsp;— whether to read water molecules&nbsp;. . . . . . . . . . . . . . . . . . . . . . . .&nbsp;73 6.4.5 IOData.convert&nbsp;modres — whether to convert modified residues&nbsp;. . . . . . . . . . . . . . . .&nbsp;73 6.4.6 IOData.hybrid36&nbsp;— whether to read PDB files conformant with hybrid-36 .&nbsp;. . . . . . . . . .&nbsp;74 6.4.7 IOData.two&nbsp;char chain — whether to read PDB files with two-character chain IDs&nbsp;. . . . . .&nbsp;74 6.4.8 IOData.atom&nbsp;files directory — search path for coordinate files&nbsp;. . . . . . . . . . . . . . . . .&nbsp;74 <br>6.5 The&nbsp;Libraries class: stereochemical parameters and molecular topology&nbsp;. . . . . . . . . . . . . . .&nbsp;75 <br>6.5.1 Libraries.topology&nbsp;— topology library information&nbsp;. . . . . . . . . . . . . . . . . . . . . . . .&nbsp;75 6.5.2 Libraries.parameters&nbsp;— parameter library information&nbsp;. . . . . . . . . . . . . . . . . . . . . .&nbsp;75 6.5.3 Topology.append()&nbsp;— append residue topology library&nbsp;. . . . . . . . . . . . . . . . . . . . . .&nbsp;75 6.5.4 Topology.clear()&nbsp;— clear residue topology library . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;75 6.5.5 Topology.read()&nbsp;— read residue topology library&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;75 6.5.6 Parameters.append()&nbsp;— append parameters library .&nbsp;. . . . . . . . . . . . . . . . . . . . . . .&nbsp;75 6.5.7 Parameters.clear()&nbsp;— clear parameters library .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;76 6.5.8 Parameters.read()&nbsp;— read parameters library&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;76 </p><p>CONTENTS </p><p>vii <br>6.5.9 Topology.make()&nbsp;— make a subset topology library .&nbsp;. . . . . . . . . . . . . . . . . . . . . . .&nbsp;76 6.5.10 Topology.submodel&nbsp;— select topology model type .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . .&nbsp;77 6.5.11 Topology.write()&nbsp;— write residue topology library&nbsp;. . . . . . . . . . . . . . . . . . . . . . . .&nbsp;77 <br>6.6 The&nbsp;Model class: handling of atomic coordinates, and model building .&nbsp;. . . . . . . . . . . . . . . . .&nbsp;78 <br>6.6.1 Model()&nbsp;— create a new 3D model&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;78 6.6.2 Model.seq&nbsp;id — sequence identity between the model and templates&nbsp;. . . . . . . . . . . . . .&nbsp;78 6.6.3 Model.resolution&nbsp;— resolution of protein structure&nbsp;. . . . . . . . . . . . . . . . . . . . . . . .&nbsp;78 6.6.4 Model.last&nbsp;energy — last objective function value .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . .&nbsp;78 6.6.5 Model.remark&nbsp;— text remark(s)&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;78 6.6.6 Model.restraints&nbsp;— all static restraints which act on the model&nbsp;. . . . . . . . . . . . . . . . .&nbsp;78 6.6.7 Model.group&nbsp;restraints — all restraints which act on atom groups&nbsp;. . . . . . . . . . . . . . .&nbsp;79 6.6.8 Model.atoms&nbsp;— all atoms in the model&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;79 6.6.9 Model.point()&nbsp;— return a point in Cartesian space&nbsp;. . . . . . . . . . . . . . . . . . . . . . . .&nbsp;79 6.6.10 Model.atom&nbsp;range() — return a subset of all atoms .&nbsp;. . . . . . . . . . . . . . . . . . . . . . .&nbsp;79 6.6.11 Model.residue&nbsp;range() — return a subset of all residues&nbsp;. . . . . . . . . . . . . . . . . . . . .&nbsp;79 6.6.12 Model.get&nbsp;insertions() — return a list of all insertions&nbsp;. . . . . . . . . . . . . . . . . . . . . .&nbsp;80 6.6.13 Model.get&nbsp;deletions() — return a list of all deletions&nbsp;. . . . . . . . . . . . . . . . . . . . . . .&nbsp;80 6.6.14 Model.loops()&nbsp;— return a list of all loops&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;80 6.6.15 Model.read()&nbsp;— read coordinates for MODEL .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;80 6.6.16 Model.build&nbsp;sequence() — build model from a sequence of one-letter codes&nbsp;. . . . . . . . . .&nbsp;82 6.6.17 Model.write()&nbsp;— write MODEL .&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;82 6.6.18 Model.clear&nbsp;topology() — clear model topology . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;83 6.6.19 Model.generate&nbsp;topology() — generate MODEL topology&nbsp;. . . . . . . . . . . . . . . . . . . .&nbsp;83 6.6.20 Model.make&nbsp;valid pdb coordinates() — make coordinates fit in PDB format .&nbsp;. . . . . . . . .&nbsp;84 6.6.21 Model.write&nbsp;psf() — write molecular topology to PSF file&nbsp;. . . . . . . . . . . . . . . . . . . .&nbsp;84 6.6.22 Model.patch()&nbsp;— patch MODEL topology . . . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;85 6.6.23 Model.patch&nbsp;ss templates() — guess MODEL disulfides from templates&nbsp;. . . . . . . . . . . .&nbsp;85 6.6.24 Model.patch&nbsp;ss() — guess MODEL disulfides from model structure .&nbsp;. . . . . . . . . . . . . .&nbsp;87 6.6.25 Model.build()&nbsp;— build MODEL coordinates from topology&nbsp;. . . . . . . . . . . . . . . . . . .&nbsp;87 6.6.26 Model.transfer&nbsp;xyz() — copy templates’ coordinates to MODEL&nbsp;. . . . . . . . . . . . . . . .&nbsp;88 6.6.27 Model.res&nbsp;num from() — residue numbers from MODEL2 to MODEL&nbsp;. . . . . . . . . . . . .&nbsp;90 6.6.28 Model.rename&nbsp;segments() — rename MODEL segments&nbsp;. . . . . . . . . . . . . . . . . . . . .&nbsp;90 6.6.29 Model.to&nbsp;iupac() — standardize certain dihedral angles&nbsp;. . . . . . . . . . . . . . . . . . . . .&nbsp;91 6.6.30 Model.reorder&nbsp;atoms() — standardize order of MODEL atoms&nbsp;. . . . . . . . . . . . . . . . .&nbsp;91 6.6.31 Model.orient()&nbsp;— center and orient MODEL&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;92 6.6.32 Model.write&nbsp;data() — write derivative model data&nbsp;. . . . . . . . . . . . . . . . . . . . . . . .&nbsp;93 6.6.33 Model.make&nbsp;region() — define a random surface patch of atoms&nbsp;. . . . . . . . . . . . . . . .&nbsp;95 6.6.34 Model.color()&nbsp;— color MODEL according to alignment&nbsp;. . . . . . . . . . . . . . . . . . . . .&nbsp;95 6.6.35 Model.make&nbsp;chains() — Fetch sequences from PDB file&nbsp;. . . . . . . . . . . . . . . . . . . . .&nbsp;97 6.6.36 Model.saxs&nbsp;intens() — Calculate SAXS intensity from model&nbsp;. . . . . . . . . . . . . . . . . .&nbsp;97 6.6.37 Model.saxs&nbsp;pr() — Calculate P(r) of model&nbsp;. . . . . . . . . . . . . . . . . . . . . . . . . . . .&nbsp;97 6.6.38 Model.saxs&nbsp;chifun() — Calculate SAXS score chi from model&nbsp;. . . . . . . . . . . . . . . . . .&nbsp;97 6.6.39 Model.assess&nbsp;ga341() — assess a model with the GA341 method&nbsp;. . . . . . . . . . . . . . . .&nbsp;97 viii </p>