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MODELLER 10.1 Manual MODELLER A Program for Protein Structure Modeling Release 10.1, r12156 Andrej Saliˇ with help from 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, Azat Badretdinov, Francisco Melo, John P. Overington, and Eric Feyfant email: modeller-care AT salilab.org URL https://salilab.org/modeller/ 2021/03/12 ii Contents Copyright notice xxi Acknowledgments xxv 1 Introduction 1 1.1 What is Modeller?............................................. 1 1.2 Modeller bibliography....................................... .... 2 1.3 Obtainingandinstallingtheprogram. .................... 3 1.4 Bugreports...................................... ............ 4 1.5 Method for comparative protein structure modeling by Modeller ................... 5 1.6 Using Modeller forcomparativemodeling. ... 8 1.6.1 Preparinginputfiles . ............. 8 1.6.2 Running Modeller ......................................... 9 2 Automated comparative modeling with AutoModel 11 2.1 Simpleusage ..................................... ............ 11 2.2 Moreadvancedusage............................... .............. 12 2.2.1 Including water molecules, HETATM residues, and hydrogenatoms .............. 12 2.2.2 Changing the default optimization and refinement protocol ................... 14 2.2.3 Getting a very fast and approximate model . ................. 14 2.2.4 Building a model from multiple templates . .................. 15 2.2.5 Buildinganallhydrogenmodel . ............... 16 2.2.6 Refiningonlypartofthemodel. .............. 16 2.2.7 Includingdisulfidebridges . ................ 18 2.2.8 Generating new-style PDBx/mmCIF outputs . ................. 19 2.2.9 Providingyourownrestraintsfile . ................. 19 2.2.10 Usingyourowninitialmodel . ............... 20 2.2.11 Adding additional restraints to the defaults . ...................... 21 2.2.12 Buildingmulti-chainmodels. ................. 22 2.2.13 Residues and chains in multi-chain models . .................... 23 2.2.14 Accessing output data after modeling is complete . ...................... 24 2.2.15 Fully automated alignment and modeling . .................. 25 2.3 Loopoptimization ................................ .............. 26 2.3.1 Automatic loop refinement after model building . .................... 26 2.3.2 Definingloopregionsforrefinement . ................ 27 iii iv CONTENTS 2.3.3 RefininganexistingPDBfile . ............. 28 3 Frequently asked questions and history 31 3.1 Frequently asked questions (FAQ) and examples . ..................... 31 3.2 Modeller updates ............................................ 38 3.2.1 Changessincerelease10.0 . ............... 38 3.2.2 Changessincerelease9.25 . ............... 38 4 Comparative modeling class reference 39 4.1 AutoModel reference .......................................... 39 4.1.1 AutoModel() — prepare to build one or more comparative models ............... 39 4.1.2 AutoModel.library schedule—selectoptimizationschedule . 40 4.1.3 AutoModel.md level—controlthemodelrefinementlevel . 40 4.1.4 AutoModel.outputs — all output data for generated models................... 40 4.1.5 AutoModel.rand method — control initial model randomization . 40 4.1.6 AutoModel.generate method—controlinitialmodelgeneration. 40 4.1.7 AutoModel.max var iterations — select length of optimizations . 41 4.1.8 AutoModel.repeat optimization — number of times to repeat optimization . ..... 41 4.1.9 AutoModel.max molpdf—objectivefunctioncutoff . 41 4.1.10 AutoModel.initial malign3d—initialtemplatealignment . 41 4.1.11 AutoModel.starting model—firstmodeltobuild. 41 4.1.12 AutoModel.ending model—lastmodeltobuild . 41 4.1.13 AutoModel.final malign3d—finaltemplate-modelalignment . 41 4.1.14 AutoModel.write intermediates — write intermediate files during optimization ........ 41 4.1.15 AutoModel.trace output—controloptimizationoutput . 41 4.1.16 AutoModel.max ca ca distance — Distance cutoff for CA-CA homology-derived restraints . 42 4.1.17 AutoModel.max n o distance — Distance cutoff for N-O homology-derived restraints..... 42 4.1.18 AutoModel.max sc mc distance — Distance cutoff for sidechain-mainchain homology-derived restraints 42 4.1.19 AutoModel.max sc sc distance — Distance cutoff for sidechain-sidechain homology-derived restraints 42 4.1.20 AutoModel.blank single chain — Control chain ID for single-chain models . 42 4.1.21 AutoModel.set output model format()—setformatforoutputmodels. 42 4.1.22 AutoModel.get optimize actions() — get actions to carry out during the initial optimization . 43 4.1.23 AutoModel.get refine actions() — get actions to carry out during the refinement . 43 4.1.24 AutoModel.select atoms() — select region for optimization and assessment . ....... 43 4.1.25 AutoModel.auto align() — generate an automatic initial alignment . ....... 43 4.1.26 AutoModel.very fast()—requestrapidoptimization . 43 4.1.27 AutoModel.make() —buildallmodels . ................. 43 4.1.28 AutoModel.cluster() — cluster all built models . ...................... 44 4.1.29 AutoModel.special restraints()—addadditionalrestraints . 44 4.1.30 AutoModel.nonstd restraints()—addrestraintsonligands . 44 4.1.31 AutoModel.special patches() — add additional patches to the topology . 44 4.1.32 AutoModel.user after single model()—analyzeorrefineeachmodel . 45 4.1.33 AutoModel.get model filename()—getthemodelPDB/mmCIFname. 45 4.1.34 AutoModel.use parallel job()—parallelizemodelbuilding. 45 CONTENTS v 4.1.35 AutoModel.guess atom types() — automatically assign Charmm atomtypes . 45 4.1.36 AutoModel.guess atom type() — automatically assign Charmm atomtype .......... 45 4.2 AllHModel reference .......................................... 46 4.2.1 AllHModel() — prepare to build all-hydrogen models . .................... 46 4.3 LoopModel reference .......................................... 46 4.3.1 LoopModel() — prepare to build models with loop refinement.................. 46 4.3.2 LoopModel.loop.md level — control the loop model refinement level . 46 4.3.3 LoopModel.loop.max var iterations — select length of optimizations . 46 4.3.4 LoopModel.loop.library schedule—selectoptimizationschedule . 47 4.3.5 LoopModel.loop.starting model—firstloopmodeltobuild . 47 4.3.6 LoopModel.loop.ending model—lastloopmodeltobuild . 47 4.3.7 LoopModel.loop.write selection only — write PDB/mmCIFs containing only the loops . 47 4.3.8 LoopModel.loop.write defined only — only write non-loop atoms present in the input model 47 4.3.9 LoopModel.loop.outputs — all output data for generatedloopmodels . 47 4.3.10 LoopModel.select loop atoms() — select region for loop optimization and assessment..... 47 4.3.11 LoopModel.get loop model filename() — get the model PDB/mmCIF name . 48 4.3.12 LoopModel.user after single loop model() — analyze or refine each loop model . 48 4.3.13 LoopModel.read potential() — read in the loop modeling potential . ...... 48 4.3.14 LoopModel.build ini loop() — create the initial conformation of the loop . 48 4.4 DOPELoopModel reference .......................................... 48 4.4.1 DOPELoopModel() — prepare to build models with DOPE looprefinement. 49 4.5 DOPEHRLoopModel reference ......................................... 49 5 Modeller general reference 51 5.1 Miscellaneous rules and features of Modeller .............................. 51 5.1.1 Modeller system.......................................... 51 5.1.2 Controlling breakpoints and the amount of output . .................... 51 5.1.3 Filenaming.................................... .......... 51 5.1.4 Filetypes ..................................... .......... 53 5.2 Stereochemical parameters and molecular topology . ........................ 54 5.2.1 Modeling residues with non-existing or incomplete entries in the topology and parameter libraries 54 5.3 Spatialrestraints ............................... ................ 55 5.3.1 Specificationofrestraints . ................ 55 5.3.2 Specificationofpseudoatoms . ............... 58 5.3.3 Excludedpairs ................................. ........... 59 5.3.4 Rigidbodies ................................... .......... 60 5.3.5 Symmetryrestraints . ............. 61 6 Modeller command reference 65 6.1 Keyforcommanddescriptions . ................ 65 6.2 The Environ class: Modeller environment ............................... 65 6.2.1 Environ() — create a new Modeller environment........................ 65 6.2.2 Environ.io — default input parameters. .................. 66 6.2.3 Environ.edat — default objective function parameters ...................... 66 vi CONTENTS 6.2.4 Environ.libs — Modeller libraries ................................ 66 6.2.5 Environ.schedule scale—energyfunctionscalingfactors. 66 6.2.6 Environ.dendrogram()—clustering . ................. 66 6.2.7 Environ.principal components()—clustering . 66 6.2.8 Environ.system() — execute system command . ................. 67 6.2.9 Environ.make pssmdb() — Create a database of PSSMs given a list of profiles . ....... 67 6.3 The EnergyData class: objectivefunctionparameters. ......... 69 6.3.1 EnergyData() — create a new set of objective function parameters ............... 69 6.3.2 EnergyData.contact shell—nonbonddistancecutoff. 69 6.3.3 EnergyData.update dynamic — nonbond recalculation threshold . 69 6.3.4 EnergyData.sphere stdv—soft-spherestandarddeviation . 70 6.3.5 EnergyData.dynamic sphere — calculate soft-sphere overlap restraints . ...... 70 6.3.6 EnergyData.dynamic lennard — calculate Lennard-Jones restraints . 70 6.3.7 EnergyData.dynamic coulomb—calculateCoulombrestraints
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