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Contents
Copyright notice xix
Acknowledgments xxi
1 Introduction 1
1.1 What is Modeller? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Modeller bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.3 Obtaining and installing the program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.4 Bug reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.5 Method for comparative protein structure modeling by Modeller . . . . . . . . . . . . . . . . . . . 5
1.6 Using Modeller for comparative modeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.6.1 Preparing input files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.6.2 Running Modeller . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2 Automated comparative modeling with automodel 11
2.1 Simple usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.2 More advanced usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.2.1 Including water molecules, HETATM residues, and hydrogen atoms . . . . . . . . . . . . . . 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 Building an all hydrogen model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.2.6 Refining only part of the model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.2.7 Including disulfide bridges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.2.8 Providing your own restraints file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.2.9 Using your own initial model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.2.10 Adding additional restraints to the defaults . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.2.11 Building multi-chain models with symmetry . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.2.12 Accessing output data after modeling is complete . . . . . . . . . . . . . . . . . . . . . . . . . 22
2.2.13 Fully automated alignment and modeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.3 Loop optimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2.3.1 Automatic loop refinement after model building . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2.3.2 Defining loop regions for refinement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.3.3 Refining an existing PDB file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
iii
iv CONTENTS
3 Frequently asked questions and history 27
3.1 Frequently asked questions (FAQ) and examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
3.2 Modeller updates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
3.2.1 Changes since release 9v7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
3.2.2 Changes since release 9v6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
4 Comparative modeling class reference 37
4.1 automodel reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
4.1.1 automodel() — prepare to build one or more comparative models . . . . . . . . . . . . . . . . 37
4.1.2 automodel.library schedule — select optimization schedule . . . . . . . . . . . . . . . . . . . . 38
4.1.3 automodel.md level — control the model refinement level . . . . . . . . . . . . . . . . . . . . 38
4.1.4 automodel.outputs — all output data for generated models . . . . . . . . . . . . . . . . . . . 38
4.1.5 automodel.rand method — control initial model randomization . . . . . . . . . . . . . . . . . 38
4.1.6 automodel.generate method — control initial model generation . . . . . . . . . . . . . . . . . 38
4.1.7 automodel.max var iterations — select length of optimizations . . . . . . . . . . . . . . . . . 38
4.1.8 automodel.repeat optimization — number of times to repeat optimization . . . . . . . . . . . 38
4.1.9 automodel.max molpdf — objective function cutoff . . . . . . . . . . . . . . . . . . . . . . . . 39
4.1.10 automodel.initial malign3d — initial template alignment . . . . . . . . . . . . . . . . . . . . . 39
4.1.11 automodel.starting model — first model to build . . . . . . . . . . . . . . . . . . . . . . . . . 39
4.1.12 automodel.ending model — last model to build . . . . . . . . . . . . . . . . . . . . . . . . . . 39
4.1.13 automodel.final malign3d — final template-model alignment . . . . . . . . . . . . . . . . . . . 39
4.1.14 automodel.write intermediates — write intermediate files during optimization . . . . . . . . . 39
4.1.15 automodel.trace output — control optimization output . . . . . . . . . . . . . . . . . . . . . 39
4.1.16 automodel.max ca ca distance — Distance cutoff for CA-CA homology-derived restraints . . 39
4.1.17 automodel.max n o distance — Distance cutoff for N-O homology-derived restraints . . . . . 40
4.1.18 automodel.max sc mc distance — Distance cutoff for sidechain-mainchain homology-derived restraints 40
4.1.19 automodel.max sc sc distance — Distance cutoff for sidechain-sidechain homology-derived restraints 40
4.1.20 automodel.get optimize actions() — get actions to carry out during the initial optimization . 40
4.1.21 automodel.get refine actions() — get actions to carry out during the refinement . . . . . . . . 40
4.1.22 automodel.select atoms() — select region for optimization . . . . . . . . . . . . . . . . . . . . 40
4.1.23 automodel.auto align() — generate an automatic initial alignment . . . . . . . . . . . . . . . 41
4.1.24 automodel.very fast() — request rapid optimization . . . . . . . . . . . . . . . . . . . . . . . 41
4.1.25 automodel.make() — build all models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
4.1.26 automodel.cluster() — cluster all built models . . . . . . . . . . . . . . . . . . . . . . . . . . 41
4.1.27 automodel.special restraints() — add additional restraints . . . . . . . . . . . . . . . . . . . . 41
4.1.28 automodel.nonstd restraints() — add restraints on ligands . . . . . . . . . . . . . . . . . . . . 41
4.1.29 automodel.special patches() — add additional patches to the topology . . . . . . . . . . . . . 42
4.1.30 automodel.user after single model() — analyze or refine each model . . . . . . . . . . . . . . 42
4.1.31 automodel.get model filename() — get the model PDB name . . . . . . . . . . . . . . . . . . 42
4.1.32 automodel.use parallel job() — parallelize model building . . . . . . . . . . . . . . . . . . . . 42
4.2 allhmodel reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
4.2.1 allhmodel() — prepare to build all-hydrogen models . . . . . . . . . . . . . . . . . . . . . . . 43
4.3 loopmodel reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
4.3.1 loopmodel() — prepare to build models with loop refinement . . . . . . . . . . . . . . . . . . 43
CONTENTS v
4.3.2 loopmodel.loop.md level — control the loop model refinement level . . . . . . . . . . . . . . . 43
4.3.3 loopmodel.loop.max var iterations — select length of optimizations . . . . . . . . . . . . . . . 43
4.3.4 loopmodel.loop.library schedule — select optimization schedule . . . . . . . . . . . . . . . . . 43
4.3.5 loopmodel.loop.starting model — first loop model to build . . . . . . . . . . . . . . . . . . . . 44
4.3.6 loopmodel.loop.ending model — last loop model to build . . . . . . . . . . . . . . . . . . . . 44
4.3.7 loopmodel.loop.write selection only — write PBDs containing only the loops . . . . . . . . . 44
4.3.8 loopmodel.loop.outputs — all output data for generated loop models . . . . . . . . . . . . . . 44
4.3.9 loopmodel.select loop atoms() — select region for loop optimization . . . . . . . . . . . . . . 44
4.3.10 loopmodel.get loop model filename() — get the model PDB name . . . . . . . . . . . . . . . 44
4.3.11 loopmodel.user after single loop model() — analyze or refine each loop model . . . . . . . . . 44
4.3.12 loopmodel.read potential() — read in the loop modeling potential . . . . . . . . . . . . . . . 45
4.3.13 loopmodel.build ini loop() — create the initial conformation of the loop . . . . . . . . . . . . 45
4.4 dope loopmodel reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
4.4.1 dope loopmodel() — prepare to build models with DOPE loop refinement . . . . . . . . . . . 45
4.5 dopehr loopmodel reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
5 Modeller general reference 47
5.1 Miscellaneous rules and features of Modeller . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
5.1.1 Modeller system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
5.1.2 Controlling breakpoints and the amount of output . . . . . . . . . . . . . . . . . . . . . . . . 47
5.1.3 File naming . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
5.1.4 File types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
5.2 Stereochemical parameters and molecular topology . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
5.2.1 Modeling residues with non-existing or incomplete entries in the topology and parameter libraries 49
5.3 Spatial restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
5.3.1 Specification of restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
5.3.2 Specification of pseudo atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
5.3.3 Excluded pairs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
5.3.4 Rigid bodies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
5.3.5 Symmetry restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
6 Modeller command reference 61
6.1 Key for command descriptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
6.2 The environ class: Modeller environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
6.2.1 environ() — create a new Modeller environment . . . . . . . . . . . . . . . . . . . . . . . . 61
6.2.2 environ.io — default input parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
6.2.3 environ.edat — default objective function parameters . . . . . . . . . . . . . . . . . . . . . . 62
6.2.4 environ.libs — Modeller libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
6.2.5 environ.schedule scale — energy function scaling factors . . . . . . . . . . . . . . . . . . . . . 62
6.2.6 environ.dendrogram() — clustering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
6.2.7 environ.principal components() — clustering . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
6.2.8 environ.system() — execute system command . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
6.2.9 environ.make pssmdb() — Create a database of PSSMs given a list of profiles . . . . . . . . . 63
6.3 The energy data class: objective function parameters . . . . . . . . . . . . . . . . . . . . . . . . . . 65
vi CONTENTS
6.3.1 energy data() — create a new set of objective function parameters . . . . . . . . . . . . . . . 65
6.3.2 energy data.contact shell — nonbond distance cutoff . . . . . . . . . . . . . . . . . . . . . . . 65
6.3.3 energy data.update dynamic — nonbond recalculation threshold . . . . . . . . . . . . . . . . 65
6.3.4 energy data.sphere stdv — soft-sphere standard deviation . . . . . . . . . . . . . . . . . . . . 66
6.3.5 energy data.dynamic sphere — calculate soft-sphere overlap restraints . . . . . . . . . . . . . 66
6.3.6 energy data.dynamic lennard — calculate Lennard-Jones restraints . . . . . . . . . . . . . . . 66
6.3.7 energy data.dynamic coulomb — calculate Coulomb restraints . . . . . . . . . . . . . . . . . 66
6.3.8 energy data.dynamic modeller — calculate non-bonded spline restraints . . . . . . . . . . . . 66
6.3.9 energy data.excl local — exclude certain local pairs of atoms . . . . . . . . . . . . . . . . . . 66
6.3.10 energy data.radii factor — scale atomic radii . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
6.3.11 energy data.lennard jones switch — Lennard-Jones switching parameters . . . . . . . . . . . 66
6.3.12 energy data.coulomb switch — Coulomb switching parameters . . . . . . . . . . . . . . . . . 67
6.3.13 energy data.relative dielectric — relative dielectric . . . . . . . . . . . . . . . . . . . . . . . . 67
6.3.14 energy data.covalent cys — use disulfide bridges in residue distance . . . . . . . . . . . . . . 67
6.3.15 energy data.nonbonded sel atoms — control interaction with picked atoms . . . . . . . . . . 67
6.3.16 energy data.nlogn use — select non-bond list generation algorithm . . . . . . . . . . . . . . . 67
6.3.17 energy data.energy terms — user-defined global energy terms . . . . . . . . . . . . . . . . . . 67
6.4 The io data class: coordinate file input parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
6.4.1 io data() — create a new input parameters object . . . . . . . . . . . . . . . . . . . . . . . . 68
6.4.2 io data.hetatm — whether to read HETATM records . . . . . . . . . . . . . . . . . . . . . . . 68
6.4.3 io data.hydrogen — whether to read hydrogen atoms . . . . . . . . . . . . . . . . . . . . . . . 68
6.4.4 io data.water — whether to read water molecules . . . . . . . . . . . . . . . . . . . . . . . . . 68
6.4.5 io data.atom files directory — search path for coordinate files . . . . . . . . . . . . . . . . . . 68
6.5 The Libraries class: stereochemical parameters and molecular topology . . . . . . . . . . . . . . . 69
6.5.1 Libraries.topology — topology library information . . . . . . . . . . . . . . . . . . . . . . . . 69
6.5.2 Libraries.parameters — parameter library information . . . . . . . . . . . . . . . . . . . . . . 69
6.5.3 Topology.append() — append residue topology library . . . . . . . . . . . . . . . . . . . . . . 69
6.5.4 Topology.clear() — clear residue topology library . . . . . . . . . . . . . . . . . . . . . . . . . 69
6.5.5 Topology.read() — read residue topology library . . . . . . . . . . . . . . . . . . . . . . . . . 69
6.5.6 Parameters.append() — append parameters library . . . . . . . . . . . . . . . . . . . . . . . . 69
6.5.7 Parameters.clear() — clear parameters library . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
6.5.8 Parameters.read() — read parameters library . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
6.5.9 Topology.make() — make a subset topology library . . . . . . . . . . . . . . . . . . . . . . . . 70
6.5.10 Topology.submodel — select topology model type . . . . . . . . . . . . . . . . . . . . . . . . . 71
6.5.11 Topology.write() — write residue topology library . . . . . . . . . . . . . . . . . . . . . . . . 71
6.6 The model class: handling of atomic coordinates, and model building . . . . . . . . . . . . . . . . . . 72
6.6.1 model() — create a new 3D model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
6.6.2 model.seq id — sequence identity between the model and templates . . . . . . . . . . . . . . 72
6.6.3 model.resolution — resolution of protein structure . . . . . . . . . . . . . . . . . . . . . . . . 72
6.6.4 model.last energy — last objective function value . . . . . . . . . . . . . . . . . . . . . . . . . 72
6.6.5 model.remark — text remark(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
6.6.6 model.restraints — all static restraints which act on the model . . . . . . . . . . . . . . . . . 72
6.6.7 model.group restraints — all restraints which act on atom groups . . . . . . . . . . . . . . . . 73
CONTENTS vii
6.6.8 model.atoms — all atoms in the model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
6.6.9 model.point() — return a point in Cartesian space . . . . . . . . . . . . . . . . . . . . . . . . 73
6.6.10 model.atom range() — return a subset of all atoms . . . . . . . . . . . . . . . . . . . . . . . . 73
6.6.11 model.residue range() — return a subset of all residues . . . . . . . . . . . . . . . . . . . . . 73
6.6.12 model.get insertions() — return a list of all insertions . . . . . . . . . . . . . . . . . . . . . . 74
6.6.13 model.get deletions() — return a list of all deletions . . . . . . . . . . . . . . . . . . . . . . . 74
6.6.14 model.loops() — return a list of all loops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
6.6.15 model.read() — read coordinates for MODEL . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
6.6.16 model.build sequence() — build model from a sequence of one-letter codes . . . . . . . . . . . 75
6.6.17 model.write() — write MODEL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
6.6.18 model.clear topology() — clear model topology . . . . . . . . . . . . . . . . . . . . . . . . . . 76
6.6.19 model.generate topology() — generate MODEL topology . . . . . . . . . . . . . . . . . . . . 77
6.6.20 model.write psf() — write molecular topology to PSF file . . . . . . . . . . . . . . . . . . . . 77
6.6.21 model.patch() — patch MODEL topology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
6.6.22 model.patch ss templates() — guess MODEL disulfides from templates . . . . . . . . . . . . 78
6.6.23 model.patch ss() — guess MODEL disulfides from model structure . . . . . . . . . . . . . . . 80
6.6.24 model.build() — build MODEL coordinates from topology . . . . . . . . . . . . . . . . . . . 80
6.6.25 model.transfer xyz() — copy templates’ coordinates to MODEL . . . . . . . . . . . . . . . . 81
6.6.26 model.res num from() — residue numbers from MODEL2 to MODEL . . . . . . . . . . . . . 82
6.6.27 model.rename segments() — rename MODEL segments . . . . . . . . . . . . . . . . . . . . . 83
6.6.28 model.to iupac() — standardize certain dihedral angles . . . . . . . . . . . . . . . . . . . . . 84
6.6.29 model.reorder atoms() — standardize order of MODEL atoms . . . . . . . . . . . . . . . . . 84
6.6.30 model.orient() — center and orient MODEL . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
6.6.31 model.write data() — write derivative model data . . . . . . . . . . . . . . . . . . . . . . . . 85
6.6.32 model.make region() — define a random surface patch of atoms . . . . . . . . . . . . . . . . . 87
6.6.33 model.color() — color MODEL according to alignment . . . . . . . . . . . . . . . . . . . . . . 88
6.6.34 model.make chains() — Fetch sequences from PDB file . . . . . . . . . . . . . . . . . . . . . . 89
6.6.35 model.saxs intens() — Calculate SAXS intensity from model . . . . . . . . . . . . . . . . . . 90
6.6.36 model.saxs pr() — Calculate P(r) of model . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
6.6.37 model.saxs chifun() — Calculate SAXS score chi from model . . . . . . . . . . . . . . . . . . 90
6.6.38 model.assess ga341() — assess a model with the GA341 method . . . . . . . . . . . . . . . . 90
6.6.39 model.assess normalized dope() — assess a model with the normalized DOPE method . . . . 91
6.7 The Restraints class: static restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
6.7.1 Restraints.rigid bodies — all rigid bodies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
6.7.2 Restraints.pseudo atoms — all pseudo atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
6.7.3 Restraints.excluded pairs — all excluded pairs . . . . . . . . . . . . . . . . . . . . . . . . . . 92
6.7.4 Restraints.nonbonded pairs — all nonbonded pairs . . . . . . . . . . . . . . . . . . . . . . . . 92
6.7.5 Restraints.symmetry — all symmetry restraints . . . . . . . . . . . . . . . . . . . . . . . . . . 92
6.7.6 Restraints.symmetry.report() — report violated symmetry restraints . . . . . . . . . . . . . . 92
6.7.7 Restraints.make() — make restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
6.7.8 Restraints.make distance() — make distance restraints . . . . . . . . . . . . . . . . . . . . . . 95
6.7.9 Restraints.unpick all() — unselect all restraints . . . . . . . . . . . . . . . . . . . . . . . . . . 96
6.7.10 Restraints.clear() — delete all restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
viii CONTENTS
6.7.11 Restraints.pick() — pick restraints for selected atoms . . . . . . . . . . . . . . . . . . . . . . 96
6.7.12 Restraints.unpick redundant() — unselect redundant restraints . . . . . . . . . . . . . . . . . 97
6.7.13 Restraints.remove unpicked() — remove unselected restraints . . . . . . . . . . . . . . . . . . 98
6.7.14 Restraints.condense() — remove unselected or redundant restraints . . . . . . . . . . . . . . . 98
6.7.15 Restraints.add() — add restraint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
6.7.16 Restraints.unpick() — unselect restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
6.7.17 Restraints.reindex() — renumber model restraints using another model . . . . . . . . . . . . 99
6.7.18 Restraints.spline() — approximate restraints by splines . . . . . . . . . . . . . . . . . . . . . 100
6.7.19 Restraints.append() — read spatial restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
6.7.20 Restraints.write() — write spatial restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
6.8 The secondary structure module: secondary structure restraints . . . . . . . . . . . . . . . . . . . 102
6.8.1 alpha() — make an -helix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
6.8.2 strand() — make a -strand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
6.8.3 sheet() — make a -sheet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
6.9 The selection class: handling of sets of atom coordinates . . . . . . . . . . . . . . . . . . . . . . . . 104
6.9.1 selection() — create a new selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
6.9.2 selection.add() — add objects to selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
6.9.3 selection.extend by residue() — extend selection by residue . . . . . . . . . . . . . . . . . . . 107
6.9.4 selection.by residue() — make sure all residues are fully selected . . . . . . . . . . . . . . . . 107
6.9.5 selection.select sphere() — select all atoms within radius . . . . . . . . . . . . . . . . . . . . . 107
6.9.6 selection.only mainchain() — select only mainchain atoms . . . . . . . . . . . . . . . . . . . . 107
6.9.7 selection.only sidechain() — select only sidechain atoms . . . . . . . . . . . . . . . . . . . . . 107
6.9.8 selection.only atom types() — select only atoms of given types . . . . . . . . . . . . . . . . . 108
6.9.9 selection.only residue types() — select only atoms of given residue type . . . . . . . . . . . . 108
6.9.10 selection.only std residues() — select only standard residues . . . . . . . . . . . . . . . . . . . 108
6.9.11 selection.only no topology() — select only residues without topology . . . . . . . . . . . . . . 108
6.9.12 selection.only het residues() — select only HETATM residues . . . . . . . . . . . . . . . . . . 108
6.9.13 selection.only water residues() — select only water residues . . . . . . . . . . . . . . . . . . . 108
6.9.14 selection.only defined() — select only atoms with defined coordinates . . . . . . . . . . . . . 108
6.9.15 selection.write() — write selection coordinates to a file . . . . . . . . . . . . . . . . . . . . . . 109
6.9.16 selection.translate() — translate all coordinates . . . . . . . . . . . . . . . . . . . . . . . . . . 109
6.9.17 selection.rotate origin() — rotate coordinates about origin . . . . . . . . . . . . . . . . . . . . 109
6.9.18 selection.rotate mass center() — rotate coordinates about mass center . . . . . . . . . . . . . 109
6.9.19 selection.transform() — transform coordinates with a matrix . . . . . . . . . . . . . . . . . . 109
6.9.20 selection.mutate() — mutate selected residues . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
6.9.21 selection.randomize xyz() — randomize selected coordinates . . . . . . . . . . . . . . . . . . . 111
6.9.22 selection.superpose() — superpose model on selection given alignment . . . . . . . . . . . . . 112
6.9.23 selection.rotate dihedrals() — change dihedral angles . . . . . . . . . . . . . . . . . . . . . . . 115
6.9.24 selection.unbuild() — undefine coordinates . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
6.9.25 selection.hot atoms() — atoms violating restraints . . . . . . . . . . . . . . . . . . . . . . . . 116
6.9.26 selection.energy() — evaluate atom selection given restraints . . . . . . . . . . . . . . . . . . 117
6.9.27 selection.debug function() — test code self-consistency . . . . . . . . . . . . . . . . . . . . . . 119
6.9.28 selection.assess dope() — assess a model selection with the DOPE method . . . . . . . . . . 120
CONTENTS ix
6.9.29 selection.assess dopehr() — assess a model with the DOPE-HR method . . . . . . . . . . . . 121
6.10 The physical module: contributions to the objective function . . . . . . . . . . . . . . . . . . . . . 122
6.10.1 physical.values() — create a new set of physical values . . . . . . . . . . . . . . . . . . . . . . 122
6.11 The optimizers module: optimization of the model . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
6.11.1 conjugate gradients() — optimize atoms given restraints, with CG . . . . . . . . . . . . . . . 124
6.11.2 quasi newton() — optimize atoms with quasi-Newton minimization . . . . . . . . . . . . . . . 126
6.11.3 molecular dynamics() — optimize atoms given restraints, with MD . . . . . . . . . . . . . . . 126
6.11.4 actions.write structure() — write out the model coordinates . . . . . . . . . . . . . . . . . . . 126
6.11.5 actions.trace() — write out optimization energies, etc . . . . . . . . . . . . . . . . . . . . . . 127
6.11.6 actions.charmm trajectory() — write out a CHARMM trajectory . . . . . . . . . . . . . . . . 127
6.11.7 User-defined optimizers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
6.12 The schedule class: variable target function optimization . . . . . . . . . . . . . . . . . . . . . . . . 131
6.12.1 schedule() — create a new schedule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
6.12.2 schedule.make for model() — trim a schedule for a model . . . . . . . . . . . . . . . . . . . . 132
6.12.3 schedule.write() — write optimization schedule . . . . . . . . . . . . . . . . . . . . . . . . . . 133
6.13 The group restraints class: restraints on atom groups . . . . . . . . . . . . . . . . . . . . . . . . . 134
6.13.1 group restraints() — create a new set of group restraints . . . . . . . . . . . . . . . . . . . . . 134
6.13.2 group restraints.append() — read group restraint parameters . . . . . . . . . . . . . . . . . . 134
6.14 The gbsa module: implicit solvation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
6.14.1 gbsa.Scorer() — create a new scorer to evaluate GB/SA energies . . . . . . . . . . . . . . . . 136
6.15 The alignment class: comparison of sequences and structures . . . . . . . . . . . . . . . . . . . . . . 137
6.15.1 alignment() — create a new alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
6.15.2 alignment.comments — alignment file comments . . . . . . . . . . . . . . . . . . . . . . . . . 137
6.15.3 alignment.append() — read sequences and/or their alignment . . . . . . . . . . . . . . . . . . 137
6.15.4 alignment.clear() — delete all sequences from the alignment . . . . . . . . . . . . . . . . . . . 138
6.15.5 alignment.read one() — read sequences one by one from a file . . . . . . . . . . . . . . . . . . 138
6.15.6 alignment.check structure structure() — check template structure superpositions . . . . . . . 139
6.15.7 alignment.check sequence structure() — check sequence/structure alignment for sanity . . . . 140
6.15.8 alignment.check() — check alignment for modeling . . . . . . . . . . . . . . . . . . . . . . . . 140
6.15.9 alignment.compare with() — compare two alignments . . . . . . . . . . . . . . . . . . . . . . 141
6.15.10 alignment.append model() — copy model sequence and coordinates to alignment . . . . . . . 141
6.15.11 alignment.append sequence() — add a sequence from one-letter codes . . . . . . . . . . . . . 142
6.15.12 alignment.append profile() — add profile sequences to the alignment . . . . . . . . . . . . . . 142
6.15.13 alignment.write() — write sequences and/or their alignment . . . . . . . . . . . . . . . . . . . 143
6.15.14 alignment.edit() — edit overhangs in alignment . . . . . . . . . . . . . . . . . . . . . . . . . . 144
6.15.15 alignment.describe() — describe proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
6.15.16 alignment.id table() — calculate percentage sequence identities . . . . . . . . . . . . . . . . . 145
6.15.17 alignment.compare sequences() — compare sequences in alignment . . . . . . . . . . . . . . . 146
6.15.18 alignment.align() — align two (blocks of) sequences . . . . . . . . . . . . . . . . . . . . . . . 146
6.15.19 alignment.align2d() — align sequences with structures . . . . . . . . . . . . . . . . . . . . . . 148
6.15.20 alignment.malign() — align two or more sequences . . . . . . . . . . . . . . . . . . . . . . . . 149
6.15.21 alignment.consensus() — consensus sequence alignment . . . . . . . . . . . . . . . . . . . . . 150
6.15.22 alignment.compare structures() — compare 3D structures given alignment . . . . . . . . . . . 151
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6.15.23 alignment.align3d() — align two structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
6.15.24 alignment.malign3d() — align two or more structures . . . . . . . . . . . . . . . . . . . . . . 153
6.15.25 alignment.salign() — align two or more sequences/structures of proteins . . . . . . . . . . . . 154
6.15.26 alignment.get suboptimals() — parse suboptimal alignments file . . . . . . . . . . . . . . . . 164
6.15.27 alignment.to profile() — convert alignment to profile format . . . . . . . . . . . . . . . . . . . 164
6.15.28 alignment.segment matching() — align segments . . . . . . . . . . . . . . . . . . . . . . . . . 165
6.16 The Sequence class: a single sequence within an alignment . . . . . . . . . . . . . . . . . . . . . . . 167
6.16.1 Sequence.range — residue range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
6.16.2 Sequence.code — alignment code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
6.16.3 Sequence.atom file — PDB file name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
6.16.4 Sequence.source — source organism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
6.16.5 Sequence.name — protein name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
6.16.6 Sequence.prottyp — protein sequence type . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
6.16.7 Sequence.resolution — structure resolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
6.16.8 Sequence.rfactor — R factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
6.16.9 Sequence.residues — list of all residues in the sequence . . . . . . . . . . . . . . . . . . . . . . 168
6.16.10 Sequence.chains — list of all chains in the sequence . . . . . . . . . . . . . . . . . . . . . . . . 168
6.16.11 Sequence.transfer res prop() — transfer residue properties . . . . . . . . . . . . . . . . . . . . 168
6.16.12 Sequence.get num equiv() — get number of equivalences . . . . . . . . . . . . . . . . . . . . . 168
6.16.13 Sequence.get sequence identity() — get sequence identity . . . . . . . . . . . . . . . . . . . . 168
6.17 The Structure class: a template structure within an alignment . . . . . . . . . . . . . . . . . . . . . 170
6.17.1 Structure.write() — write out PDB file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
6.17.2 Structure.reread() — reread coordinates from atom file . . . . . . . . . . . . . . . . . . . . . 170
6.18 The Chain class: a single chain in a model or alignment . . . . . . . . . . . . . . . . . . . . . . . . . 171
6.18.1 Chain.name — chain ID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
6.18.2 Chain.residues — all residues in the chain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
6.18.3 Chain.atoms — all atoms in the chain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
6.18.4 Chain.filter() — check if this chain passes all criteria . . . . . . . . . . . . . . . . . . . . . . . 171
6.18.5 Chain.write() — write out chain sequence to an alignment file . . . . . . . . . . . . . . . . . . 172
6.18.6 Chain.atom file and code() — get suitable names for this chain . . . . . . . . . . . . . . . . . 173
6.18.7 Chain.join() — join other chain(s) onto this one . . . . . . . . . . . . . . . . . . . . . . . . . 173
6.19 The Residue class: a single residue in a model or alignment . . . . . . . . . . . . . . . . . . . . . . . 174
6.19.1 Residue.name — internal (CHARMM) residue type name . . . . . . . . . . . . . . . . . . . . 174
6.19.2 Residue.pdb name — PDB (IUPAC) type name . . . . . . . . . . . . . . . . . . . . . . . . . 174
6.19.3 Residue.code — One-letter residue type code . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
6.19.4 Residue.hetatm — HETATM indicator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
6.19.5 Residue.index — internal integer index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
6.19.6 Residue.num — PDB-style residue number . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
6.19.7 Residue.curvature — Mainchain curvature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
6.19.8 Residue.atoms — all atoms in the residue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
6.19.9 Residue.chain — chain object . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
6.19.10Residue.phi —  dihedral angle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
6.19.11Residue.psi —   dihedral angle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
CONTENTS xi
6.19.12Residue.omega — ! dihedral angle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
6.19.13Residue.alpha —  dihedral angle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
6.19.14Residue.chi1 — 1 dihedral angle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
6.19.15Residue.chi2 — 2 dihedral angle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
6.19.16Residue.chi3 — 3 dihedral angle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
6.19.17Residue.chi4 — 4 dihedral angle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
6.19.18Residue.chi5 — 5 dihedral angle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
6.19.19Residue.get aligned residue() — get aligned residue in another sequence . . . . . . . . . . . . 176
6.19.20Residue.add leading gaps() — add gap(s) before this residue . . . . . . . . . . . . . . . . . . 177
6.19.21Residue.add trailing gaps() — add gap(s) after this residue . . . . . . . . . . . . . . . . . . . 177
6.19.22Residue.remove leading gaps() — remove gap(s) before this residue . . . . . . . . . . . . . . . 177
6.19.23Residue.remove trailing gaps() — remove gap(s) after this residue . . . . . . . . . . . . . . . 177
6.19.24Residue.get leading gaps() — get number of gaps before this residue . . . . . . . . . . . . . . 177
6.19.25Residue.get trailing gaps() — get number of gaps after this residue . . . . . . . . . . . . . . . 177
6.20 The Dihedral class: a single dihedral in a model or alignment . . . . . . . . . . . . . . . . . . . . . 178
6.20.1 Dihedral.value — current value in degrees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
6.20.2 Dihedral.atoms — atoms defining the angle . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
6.20.3 Dihedral.dihclass — integer dihedral class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
6.21 The Point class: a point in Cartesian space . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
6.21.1 Point.x — x coordinate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
6.21.2 Point.select sphere() — select all atoms within radius . . . . . . . . . . . . . . . . . . . . . . 179
6.22 The Atom class: a single atom in a model or structure . . . . . . . . . . . . . . . . . . . . . . . . . . 180
6.22.1 Atom.dvx — objective function derivative . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
6.22.2 Atom.vx — x component of velocity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
6.22.3 Atom.biso — isotropic temperature factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
6.22.4 Atom.occ — occupancy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
6.22.5 Atom.charge — electrostatic charge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
6.22.6 Atom.mass — mass . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
6.22.7 Atom.name — PDB name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
6.22.8 Atom.element — Element symbol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
6.22.9 Atom.residue — residue object . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
6.23 The profile class: using sequence profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
6.23.1 profile() — create a new profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
6.23.2 profile.read() — read a profile of a sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
6.23.3 profile.write() — write a profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
6.23.4 profile.to alignment() — profile to alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
6.23.5 profile.scan() — Compare a target profile against a database of profiles . . . . . . . . . . . . 184
6.23.6 profile.build() — Build a profile for a given sequence or alignment . . . . . . . . . . . . . . . 186
6.23.7 pssmdb() — create a new PSSM database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
6.23.8 pssmdb.read() — read a PSSM database from a file . . . . . . . . . . . . . . . . . . . . . . . 188
6.24 The sequence db class: using sequence databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
6.24.1 sequence db() — create a new sequence database . . . . . . . . . . . . . . . . . . . . . . . . . 189
6.24.2 sequence db.read() — read a database of sequences . . . . . . . . . . . . . . . . . . . . . . . . 189
xii CONTENTS
6.24.3 sequence db.write() — write a database of sequences . . . . . . . . . . . . . . . . . . . . . . . 190
6.24.4 sequence db.convert() — convert a database to binary format . . . . . . . . . . . . . . . . . . 190
6.24.5 sequence db.search() — search for similar sequences . . . . . . . . . . . . . . . . . . . . . . . 190
6.24.6 sequence db.filter() — cluster sequences by sequence-identity . . . . . . . . . . . . . . . . . . 192
6.25 The density class: handling electron microscopy density data . . . . . . . . . . . . . . . . . . . . . . 194
6.25.1 density() — create a new density map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
6.25.2 density.read() — read an EM (electron microscopy) density map file . . . . . . . . . . . . . . 194
6.25.3 density.grid search() — dock a structure into an EM (electron microscopy) density map . . . 194
6.26 The saxsdata class: using small-angle X-ray (SAXS) data . . . . . . . . . . . . . . . . . . . . . . . . 197
6.26.1 saxsdata() — create a new saxsdata structure . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
6.26.2 saxsdata.ini saxs() — Initialization of SAXS data . . . . . . . . . . . . . . . . . . . . . . . . . 197
6.26.3 saxsdata.saxs read() — Read in SAXS data . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
6.26.4 saxsdata.saxs pr read() — Read in P(r) data . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
6.27 The info object: obtaining information about the Modeller build . . . . . . . . . . . . . . . . . . 199
6.27.1 info.version — the full Modeller version number . . . . . . . . . . . . . . . . . . . . . . . . 199
6.27.2 info.version info — the version number, as a tuple . . . . . . . . . . . . . . . . . . . . . . . . 199
6.27.3 info.build date — the date this binary was built . . . . . . . . . . . . . . . . . . . . . . . . . 199
6.27.4 info.exe type — the executable type of this binary . . . . . . . . . . . . . . . . . . . . . . . . 199
6.27.5 info.debug — this binary’s debug flag . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
6.27.6 info.bindir — Modeller binary directory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
6.27.7 info.time mark() — print current date, time, and CPU time . . . . . . . . . . . . . . . . . . . 199
6.27.8 info.jobname — name of the current job . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
6.28 The log object: controlling the amount of output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
6.28.1 log.level() — Set all log output levels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
6.28.2 log.none() — display no log output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
6.28.3 log.minimal() — display minimal log output . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
6.28.4 log.verbose() — display verbose log output . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
6.28.5 log.very verbose() — display verbose log output, and dynamic memory information . . . . . 200
6.29 The modfile module: handling of files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
6.29.1 modfile.default() — generate an ‘automatic’ filename . . . . . . . . . . . . . . . . . . . . . . . 201
6.29.2 modfile.delete() — delete a file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
6.29.3 modfile.inquire() — check if file exists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
6.29.4 modfile.File() — open a handle to a Modeller file . . . . . . . . . . . . . . . . . . . . . . . 201
6.30 The scripts module: utility scripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
6.30.1 cispeptide() — creates cis-peptide stereochemical restraints . . . . . . . . . . . . . . . . . . . 202
6.30.2 complete pdb() — read a PDB file, and fill in any missing atoms . . . . . . . . . . . . . . . . 202
6.31 The salign module: high-level usage of SALIGN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
6.31.1 iterative structural align() — obtain the best structural alignment . . . . . . . . . . . . . . . 202
6.32 Parallel job support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
6.32.1 job() — create a new parallel job . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
6.32.2 sge pe job() — create a job using all Sun GridEngine (SGE) slave processes . . . . . . . . . . 204
6.32.3 sge qsub job() — create a job which can be expanded with Sun GridEngine ’qsub’ . . . . . . 204
6.32.4 job.slave startup commands — Slave startup commands . . . . . . . . . . . . . . . . . . . . . 204
CONTENTS xiii
6.32.5 job.queue task() — submit a task to run within the job . . . . . . . . . . . . . . . . . . . . . 204
6.32.6 job.run all tasks() — run all queued tasks, and return results . . . . . . . . . . . . . . . . . . 205
6.32.7 job.yield tasks unordered() — run all queued tasks, and yield unordered results . . . . . . . . 206
6.32.8 job.start() — start all slaves for message-passing . . . . . . . . . . . . . . . . . . . . . . . . . 206
6.32.9 Communicator.send data() — send data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
6.32.10Communicator.get data() — get data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
6.32.11 slave.run cmd() — run a command on the slave . . . . . . . . . . . . . . . . . . . . . . . . . . 207
6.32.12 local slave() — create a slave running on the local machine . . . . . . . . . . . . . . . . . . . 207
6.32.13 sge pe slave() — create a slave running on a Sun GridEngine parallel environment slave node 207
6.32.14 sge qsub slave() — create a ’qsub’ slave running on a Sun GridEngine node . . . . . . . . . . 208
6.32.15 ssh slave() — create a slave on a remote host accessed via ssh . . . . . . . . . . . . . . . . . . 208
7 Modeller low-level programming 209
7.1 User-defined features and restraint forms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
7.1.1 User-defined feature types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
7.1.2 User-defined restraint forms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210
7.1.3 User-defined energy terms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212
7.2 Modeller programming interface (API) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
A Methods 217
A.1 Dynamic programming for sequence and structure comparison and searching . . . . . . . . . . . . . 217
A.1.1 Pairwise comparison . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217
A.1.2 Variable gap penalty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
A.1.3 Local versus global alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
A.1.4 Similarity versus distance scores . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
A.1.5 Multiple comparisons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
A.2 Optimization of the objective function by Modeller . . . . . . . . . . . . . . . . . . . . . . . . . . 219
A.2.1 Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
A.2.2 Optimizers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220
A.3 Equations used in the derivation of the molecular pdf . . . . . . . . . . . . . . . . . . . . . . . . . . 223
A.3.1 Features and their derivatives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
A.3.2 Restraints and their derivatives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226
A.4 Flowchart of comparative modeling by Modeller . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
A.5 Loop modeling method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231
B File formats 233
B.1 Alignment file (PIR) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
B.2 Restraints file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
B.2.1 Restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
B.2.2 Excluded pairs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
B.2.3 Pseudo atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236
B.2.4 Symmetry restraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
B.2.5 Rigid bodies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
B.3 Profile file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
B.4 Binary files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 238
xiv CONTENTS
C Converting Top scripts from old Modeller versions 239
C.1 Running old scripts unchanged . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239
C.2 Converting Top scripts to Python . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239
C.2.1 Top commands and variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239
C.2.2 Top models and alignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240
C.2.3 Top to Python correspondence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240


modeller user manual

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