Contents Menu Expand Light mode Dark mode Auto light/dark, in light mode Auto light/dark, in dark mode Skip to content
pestifer 2.5.2 documentation
pestifer 2.5.2 documentation
  • Introduction
  • Installation
  • Usage
    • config-help
    • build
      • fetch
      • continuation
      • merge
      • psfgen
        • patches
        • mutations
        • deletions
        • insertions
        • crotations
        • transrot
        • ssbonds and ssbondsdelete
        • links
        • substitutions
        • grafts
      • validate
      • pdb2pqr
      • md
      • manipulate
        • crotations
        • transrot
        • align
        • transfer_coords
      • ligate
      • cleave
      • solvate
      • make_membrane_system
      • ring_check
      • terminate
    • build-example
    • fetch-example
    • new-system
    • wheretcl
    • make-pdb-collection
    • make-ligand-mol2
    • desolvate
    • make-namd-restart
    • show-resources
    • follow-namd-log
    • mdplot
    • modify-package
    • setup-vmd
  • Examples
    • Example 1: Bovine Pancreatic Trypsin Inhibitor (BPTI)
    • Example 2: BPTI Excluding the Phosphate Ion
    • Example 3: BPTI with a Mutated-out Disulfide Bond
    • Example 4: BPTI with a Mutated-in Disulfide Bond
    • Example 5: HIV Protease with Patches to Protonate Aspartates
    • Example 6: Fasciculin 1 at pH 7.0
    • Example 7: Closed, Unliganded HIV-1 BG505 Env SOSIP.664 Trimer
    • Example 8: Closed, PGT122/35O22-Liganded HIV-1 BG505 Env SOSIP.664 Trimer (ligands removed)
    • Example 9: Cleaved, Asymmetric HIV-1 AD8 Env Ectodomain Trimer
    • Example 10: Cleaved, Asymmetric HIV-1 AE2 Env Ectodomain Trimer
    • Example 11: Open, Symmetric D9/CD4-liganded HIV-1 SOSIP Env Ectodomain Trimer (ligands removed)
    • Example 12: Open, Symmetric 17b/CD4-liganded HIV-1 B41 SOSIP Env Ectodomain Trimer
    • Example 13: DES-PHE B1 Bovine Insulin Hexamer
    • Example 14: Human Insulin Receptor Ectodomain IRαβ
    • Example 15: Fully Glycosylated, Closed SARS-CoV-2 Omicron BA.2 Variant Spike
    • Example 16: HIV-1 Env MPER-TM Trimer in a DMPC Symmetric Bilayer
    • Example 17: HIV-1 Env MPER-TM Trimer in an Asymmetric, Model Viral Bilayer
    • Example 18: E. coli Replicative DNA Polymerase Complex Bound to DNA
    • Example 19: Sperm whale myoglobin
    • Example 20: Mitochondrial methylmalonyl-CoA mutase (Alphafold P22033)
    • Example 21: Asymmetric GroEL/GroES Chaperonin Complex
    • Example 22: Ferredoxin-NADP(H) Reductase from Rhodobacter capsulatus
  • Configuration File Reference
    • charmmff
      • user_pdbcollections
      • standard
        • rtf
        • str
        • prm
      • custom
        • rtf
        • str
        • prm
      • user_custom
        • searchpath
        • rtf
        • str
        • prm
        • segtypes
    • psfgen
      • aliases
        • atom
        • residue
    • namd
      • gpu-resident
      • deprecated3
      • generic
      • vacuum
      • solvated
      • thermostat
      • barostat
      • membrane
      • harmonic
    • paths
    • tasks
      • fetch
      • continuation
      • merge
      • psfgen
        • source
          • sequence
            • build_zero_occupancy_C_termini
            • build_zero_occupancy_N_termini
            • loops
              • declash
            • glycans
              • declash
        • mods
      • ligate
        • steer
          • constraints
        • connect
      • pdb2pqr
      • mdplot
        • logs
        • figsize
        • timeseries
        • units
        • axis-labels
      • cleave
      • domainswap
      • solvate
      • desolvate
      • ring_check
        • segtypes
      • make_membrane_system
        • compute_pressure_profile
        • bilayer
          • prebuilt
          • patch_nlipids
          • composition
          • relaxation_protocols
            • patch
              • md
                • addl_paramfiles
                • other_parameters
            • quilt
              • md
                • addl_paramfiles
                • other_parameters
        • embed
      • md
        • addl_paramfiles
        • constraints
        • ssrestraints
      • manipulate
        • mods
      • terminate
        • test_standards
        • package
          • namd
            • addl_paramfiles
            • constraints
      • validate
        • tests
          • attribute_test
          • connection_test
          • residue_test
  • API
    • pestifer package
      • pestifer.charmmff package
        • pestifer.charmmff.ligand_paramgen package
          • pestifer.charmmff.ligand_paramgen.mol2_writer module
          • pestifer.charmmff.ligand_paramgen.orchestrator module
          • pestifer.charmmff.ligand_paramgen.protonation module
          • pestifer.charmmff.ligand_paramgen.rcsb module
        • pestifer.charmmff.charmmffcontent module
        • pestifer.charmmff.charmmffprm module
        • pestifer.charmmff.charmmfftop module
        • pestifer.charmmff.graphhelpers module
        • pestifer.charmmff.make_pdb_collection module
        • pestifer.charmmff.pdbrepository module
      • pestifer.cli package
        • pestifer.cli.pestifer module
        • pestifer.cli.subcommand module
      • pestifer.core package
        • pestifer.core.artifacts module
        • pestifer.core.baseobj module
        • pestifer.core.command module
        • pestifer.core.config module
        • pestifer.core.controller module
        • pestifer.core.errors module
        • pestifer.core.example module
        • pestifer.core.examplemanager module
        • pestifer.core.labels module
        • pestifer.core.objmanager module
        • pestifer.core.pipeline module
        • pestifer.core.resourcemanager module
      • pestifer.logparsers package
        • pestifer.logparsers.logparser module
        • pestifer.logparsers.namdlogparser module
        • pestifer.logparsers.packmollogparser module
        • pestifer.logparsers.pdb2pqrlogparser module
        • pestifer.logparsers.psfgenlogparser module
      • pestifer.molecule package
        • pestifer.molecule.asymmetricunit module
        • pestifer.molecule.atom module
        • pestifer.molecule.bilayer module
        • pestifer.molecule.bioassemb module
        • pestifer.molecule.chainidmanager module
        • pestifer.molecule.molecule module
        • pestifer.molecule.residue module
        • pestifer.molecule.segment module
        • pestifer.molecule.stateinterval module
        • pestifer.molecule.transform module
      • pestifer.objs package
        • pestifer.objs.align module
        • pestifer.objs.cfusion module
        • pestifer.objs.cleavagesite module
        • pestifer.objs.crot module
        • pestifer.objs.deletion module
        • pestifer.objs.graft module
        • pestifer.objs.insertion module
        • pestifer.objs.link module
        • pestifer.objs.mutation module
        • pestifer.objs.orient module
        • pestifer.objs.patch module
        • pestifer.objs.resid module
        • pestifer.objs.rottrans module
        • pestifer.objs.seqadv module
        • pestifer.objs.ssbond module
        • pestifer.objs.ssbonddelete module
        • pestifer.objs.substitution module
        • pestifer.objs.ter module
        • pestifer.objs.transfer_coords module
      • pestifer.psfutil package
        • pestifer.psfutil.psfangle module
        • pestifer.psfutil.psfatom module
        • pestifer.psfutil.psfbond module
        • pestifer.psfutil.psfcontents module
        • pestifer.psfutil.psfdihedral module
        • pestifer.psfutil.psfpairex module
        • pestifer.psfutil.psfpatch module
        • pestifer.psfutil.psfremark module
        • pestifer.psfutil.psfring module
        • pestifer.psfutil.psftopoelement module
      • pestifer.resources package
      • pestifer.schema package
      • pestifer.scripters package
        • pestifer.scripters.generic module
        • pestifer.scripters.namd module
        • pestifer.scripters.namd_colvar_input module
        • pestifer.scripters.packmol module
        • pestifer.scripters.psfgen module
        • pestifer.scripters.tcl module
        • pestifer.scripters.vmd module
      • pestifer.sphinxext package
        • pestifer.sphinxext.sphinx_examplemanager module
        • pestifer.sphinxext.task_table module
        • pestifer.sphinxext.tclscript module
        • pestifer.sphinxext.toctree_util module
      • pestifer.subcommands package
        • pestifer.subcommands.build module
        • pestifer.subcommands.build_example module
        • pestifer.subcommands.config_default module
        • pestifer.subcommands.config_help module
        • pestifer.subcommands.desolvate module
        • pestifer.subcommands.fetch_example module
        • pestifer.subcommands.follow_namd_log module
        • pestifer.subcommands.make_ligand_mol2 module
        • pestifer.subcommands.make_namd_restart module
        • pestifer.subcommands.make_pdbcollection module
        • pestifer.subcommands.mdplot module
        • pestifer.subcommands.modify_package module
        • pestifer.subcommands.new_system module
        • pestifer.subcommands.rebuild_charmmff_cache module
        • pestifer.subcommands.setup_vmd module
        • pestifer.subcommands.show_resources module
        • pestifer.subcommands.wheretcl module
      • pestifer.tasks package
        • pestifer.tasks.basetask module
        • pestifer.tasks.cleave module
        • pestifer.tasks.continuation module
        • pestifer.tasks.desolvate module
        • pestifer.tasks.domainswap module
        • pestifer.tasks.fetch module
        • pestifer.tasks.ligate module
        • pestifer.tasks.make_membrane_system module
        • pestifer.tasks.manipulate module
        • pestifer.tasks.mdplot module
        • pestifer.tasks.mdtask module
        • pestifer.tasks.merge module
        • pestifer.tasks.pdb2pqr module
        • pestifer.tasks.psfgen module
        • pestifer.tasks.pytest_buildterminate module
        • pestifer.tasks.ringcheck module
        • pestifer.tasks.solvate module
        • pestifer.tasks.taskcollections module
        • pestifer.tasks.terminate module
        • pestifer.tasks.validate module
      • pestifer.util package
        • pestifer.util.cacheable_object module
        • pestifer.util.cifutil module
        • pestifer.util.colors module
        • pestifer.util.coord module
        • pestifer.util.formatvalidator module
        • pestifer.util.gitutil module
        • pestifer.util.linkcell module
        • pestifer.util.namdrestart module
        • pestifer.util.patch module
        • pestifer.util.progress module
        • pestifer.util.pytest_plugin module
        • pestifer.util.readme_to_changelog_with_dates module
        • pestifer.util.spinner_wrapper module
        • pestifer.util.stringthings module
        • pestifer.util.units module
        • pestifer.util.util module
  • Tcl sources
    • Top-level scripts
    • Tcl scripts
    • Tcl packages
  • Changelog
Back to top
Copyright © 2023-2025, Cameron F. Abrams
Made with Sphinx and @pradyunsg's Furo
GitHub LinkedIn