Prepare

This module helps in preparing input PDB files for other MMMx modules. It can cut and merge existing structures, reorient structures based on symmetry or on constructing a coarse-grained lipid bilayer model (requires MSMS), add, repair or modify sidechains (requires SCWRL4), superimpose structures (may require MUSCLE if sequence-based), amd renumber residues. Several processing steps can be performed without saving intermediate results.

Features are demonstrated in examples demo_Prepare.mcx and demo_RBreference.mcx. The latter example is a two-module pipeline that uses module Prepare before module ExperimentDesign.

The keywords are grouped into input/output (getpdb, getcyana, save), coordinate transformations (center, symmetry, bilayer), sidegroup changes (mutate, repair, repack, deselenate) and structure editing (renumber, chains, replace, remove, merge).

The following keywords are supported:

getpdb

Input of a raw ensemble (uniform populations) by reading a single PDB file.

getpdb file identifier
Arguments
  • file - file name

  • identifier - module-internal entity identifier

Remarks
  • the PDB file can contain several models (conformers) or a single one

  • for MMMx ensemble PDB files with population information in REMARK 400, such information is read

getcyana

Input of a raw ensemble (uniform populations) by reading a single PDB file generated by CYANA.

getcyana file identifier [maxchains]
Arguments
  • file - file name

  • identifier - module-internal entity identifier

  • maxchains - reading is stopped after the specified number of chains, optional, defaults to all chains

Remarks
  • information on pseudo-residues is removed

  • standard PDB residue names are set for nucleic acids

  • parameter maxchains allows for skipping pseudo-chains that simulate only labels

  • reside types CYSS and CYSM are converted to CYS, label atoms in CYSM are skipped

save

Save a (modified) entity to a PDB file.

save file identifier [[PDB_ID] selection]
Arguments
  • file - file name

  • identifier - module-internal entity identifier

  • PDB_ID - four-character code used as PDB identifier, optional, defaults to PDB identifiert of loaded entity

  • selection - optional, if present, only a selected part of the structure is saved, see Selection by address

Remarks
  • a minimal PDF file is saved

center

Center the coordinates at the mean coordinate of all atoms

center identifier
Arguments
  • identifier - module-internal entity identifier

Remarks
  • the result is not automatically saved, use save if necessary

symmetry

Transform coordinates to a symmetry frame. This is a block key with n lines for an n-fold symmetry axis.

symmetry mode identifier
   'address_1'
   []
   'address_n'
.symmetry
Arguments
  • mode - superposition mode, can be backbone or CA or C4' or all

  • identifier - module-internal entity identifier

  • address_1 address of chain, e.g. (A) or residue range, e.g., (A)58-108 in the first protomer

  • address_n address of chain or residue range in the last protomer

Remarks
  • the addresses together with the mode define the atoms that are superimposed by minimal rmsd

  • the result is not automatically saved, use save if necessary

  • the C_n symmetry axis becomes the new z axis

bilayer

Computes a coarse-grained bilayer model and transforms coordinates into the bilayer frame.

bilayer mode orientation identifier
Arguments
  • mode - can be bundle for \alpha-helical bundles or barrel for \beta-barrels

  • orientation - can be oriented if the protein is already properly oriented or none if it is not

  • identifier - module-internal entity identifier

Remarks
  • the algorithm minimizes free energy of bilayer insertion

  • the Third-party software MSMS is required

  • the bilayer normal is the new z axis

  • if the protein can be oriemted by symmetry, beter use symmetry first and orientation mode oriented * the result is not automatically saved, use save if necessary

superimpose

Superimposes one structure onto another structure. The superposition can be defined by a subset of atom coordinates.

superimpose moving template [directive_1 [directive_2]]
Arguments
  • moving - module-internal entity identifier of the structure whose coordinates are transformed

  • template - module-internal entity identifier of the structure that serves as a template

  • directive_1 - optional directive that specifies how the superposition takes place (see Remarks)

  • directive_2 - another optional directive that specifies how the superposition takes place (see Remarks)

Remarks
  • the coordinates of the atoms specified by template fields and by directives are least-square superimposed on corresponding template coordinates

  • by default, residue numbers are assumed to match in moving and template structure, directive align matches residues by sequence alignment instead

  • by default, backbone atoms are superimposed, directive CA superimposes only C \alpha atoms, directive C4' only C4’ atoms of nucleotides, and directive all all atoms

  • part of the moving and template strucure can be selected by subfields, for instance BtuCDF.(F) selects only chain F of entity BruCDF for superposition, BtuCDF.(F)147-238 only residues 147-238 of this chain

  • selection is possible only down to residue level, not atom level

  • the whole structure moves, but only the selected part is least-squares superimposed

mutate

Mutates residues. This is a block key with each line corresponding to one residue to be mutated.

mutate identifier
   'address_1' 'new_residue_1'
   []
   'address_n' 'new_residue_n'
.mutate
Arguments
  • identifier - module-internal entity identifier

  • address_1 residue address of first residue to be mutated, see Selection by address

  • new_residue_1 three-letter or single-letter code for new sidechain of first residue

  • address_n residue address of last residue to be mutated

  • new_residue_n three-letter or single-letter code for new sidechain of last residue

Remarks

repair

Repairs all incompletely defined amino acid sidechains in an entity.

repair identifier
Arguments
  • identifier - module-internal entity identifier

Remarks

repack

Repacks all amino acid sidechains in an entity.

repack identifier
Arguments
  • identifier - module-internal entity identifier

Remarks

deselenate

Replaces selenocysteine and selenomethionine by their native counterparts cysteine and methionine.

deselenate identifier
Arguments
  • identifier - module-internal entity identifier

Remarks
  • this function does not require third-party software

  • seleno amino acids are sometimes used for easier phasing of x-ray diffraction data

renumber

Renumbers residues in one chain of an entity.

renumber address shift identifier
Arguments
  • address - a chain address, such as (A)

  • shift - offset to current residue numbers, can be negative or positive integer

  • identifier - module-internal entity identifier

Remarks
  • use several renumber lines, if you want to renumber more than one chain

chains

Restricts an entity to a subset of chains

chains address identifier
Arguments
  • address - MMMx chain address, such as (A) or (A,C,E)

  • identifier - module-internal entity identifier

Remarks
  • the entity with the given identifier is changed, but not automatically saved

  • use the save command, if necessary

replace

Replaces a chain in one entity with a chain from another entity

replace id_1.chain_1 id_2.chain_2
Arguments
  • id_1.chain_1 - identifier of target chsin, such as BtuCDF.(F) for chain F in entity BtuCDF to be replaced

  • id_2.chain_2 - identifier of template chsin, such as BtuF_CBI.(A) for using A in entity BtuF_CDI as a replacement

Remarks
  • the entity with the given identifier is changed, but not automatically saved

  • use the save command, if necessary

remove

Remove a residue

remove address idenfifier
Arguments
  • address - residue address, such as (A)238

  • identifier - module-internal entity identifier

Remarks
  • the entity with the given identifier is changed, but not automatically saved

  • use the save command, if necessary

  • use the merge command, if you wish to remove ranges of residues

merge

Merges residue ranges of chains to a new entity. The parts can stem from different entitities, thus creating a chimera. This is a block key, with each line corresponding to one part.

merge identifier
  'ID_1 address_1'
      []
  'ID_n address_n'
.merge
Arguments
  • identifier - module-internal identifier of the newly created entity

  • ID_1 identifier of the entity from which the first part is taken

  • address_1 address of the residues from which the first part is taken, e.g. {11}(A)58-146 for residues 58-146 of chain A in conformer 11

  • ID_n identifier of the entity from which the last part is taken

  • address_n address of the residues from which the last part is taken

Remarks
  • do not use an exsiting entity identifier

  • the entity with the given identifier is created, but not automatically saved

  • use the save command, if necessary