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:

`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, better use symmetry first and orientation mode oriented
the result is not automatically saved, use save if necessary

`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

`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

`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

`getAlphaFold`¶

Input of an AlphaFold prediction.

getAlphaFold UniProtID identifier

Arguments

UniProtID - UniProt identifier of the AlphaFold prediction
identifier - module-internal entity identifier

Remarks

note that not for all sequences in UniProt, AlphaFold predictions exist in the database

`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
residue types CYSS and CYSM are converted to CYS, label atoms in CYSM are skipped

`getens`¶

Input of an ensemble by reading an MMMx ensemble list (.ens)

getens file identifier

Arguments

file - file name
identifier - module-internal entity identifier

Remarks

all PDB files of conformers contained in the ensemble list must be on the Matlab path
populations (weights) of conformers are read

`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

`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 existing entity identifier
the entity with the given identifier is created, but not automatically saved
use the save command, if necessary

`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

Third-party software SCWRL4 is required
only amino acids, not nucleotides, can be mutated in this version of MMMx

`oligomer`¶

Build an oligomer from an oriented peptide chain ensemble

oligomer input N output address

Arguments

input - module-internal entity identifier for input entity
N - optional multiplicity, defaults to N = 2 (dimer)
output - basis name for output files, the filenames are $output$ -m-%i.pdb, where %i stands for the conformer number
address - optional address for chain and residue range, such as (A)128-611, chain defaults to the first chain, and range to all residues

Remarks

the input entity must be oriented, with the C_N axis of the oligomer being the z axis
from an input entity with C conformers, all C^N possible conformer combinations are generated
an ensemble list $output$ .ens with uniform populations (1/C^N) is written as well

`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

`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

`repack`¶

Repacks all amino acid sidechains in an entity.

repack identifier

Arguments

identifier - module-internal entity identifier

Remarks

Third-party software SCWRL4 is required

`repair`¶

Repairs all incompletely defined amino acid sidechains in an entity.

repair identifier

Arguments

identifier - module-internal entity identifier

Remarks

Third-party software SCWRL4 is required

`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

`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

`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

`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

Prepare¶

bilayer¶

center¶

chains¶

deselenate¶

getAlphaFold¶

getcyana¶

getens¶

getpdb¶

merge¶

mutate¶

oligomer¶

remove¶

renumber¶

repack¶

repair¶

replace¶

save¶

superimpose¶

symmetry¶

`bilayer`¶

`center`¶

`chains`¶

`deselenate`¶

`getAlphaFold`¶

`getcyana`¶

`getens`¶

`getpdb`¶

`merge`¶

`mutate`¶

`oligomer`¶

`remove`¶

`renumber`¶

`repack`¶

`repair`¶

`replace`¶

`save`¶

`superimpose`¶

`symmetry`¶