ExperimentDesign

This module helps in selecting site pairs for spectroscopic labeling. The sequence of command lines is relevant. Features are demonstrated in examples demo_ExperimentDesign.mcx and demo_RBreference.mcx. The latter example is a two-module pipeline that uses module Prepare before EperimentDesign.

The following keywords are supported:

import

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

import file identifier
Arguments
  • file - file name

  • identifier - module-internal entity identifier of this ensemble

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 discarded

addpdb

Input of a single conformer or of a raw ensemble (uniform populations) by using wildcards in the file name.

addpdb files identifier
Arguments
  • files - file name, which can include wildcards (*, ?) for ensemble input

  • identifier - module-internal entity identifier of this ensemble

Remarks
  • for ensemble input with wildcards, all PDB files must contain conformers with the same primary structure

  • a single input PDB file can contain several models (conformers), for clarity, rather use import for this case

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

getens

Input of an ensemble (with populations) from an MMMx ensemble list

getens file identifier
Arguments
  • file - file name, extension should be .ens

  • identifier - module-internal entity identifier of this ensemble

Remarks
  • keyword input is synonymous with getens

expand

Expand a rigid-body arrangement ensemble computed by the Rigi module

expand file identifier
Arguments
  • file - file name, extension should be .mat

  • identifier - module-internal entity identifier of this ensemble

Remarks
  • the whole ensemble will be built in memory, be cautious with very large ensembles

plot

Requests that any generated plots are saved as graphics files.

plot file extension
Arguments
  • file - basis file name, from which all plot file names are derived

  • format - graphics format

Remarks
  • possible graphics formats are ‘pdb’, ‘png’, ‘epsc’ (encapsulated postscript), ‘jpg’, ‘bmp’, ‘emf’ (enhanced metafile), ‘tif’

  • from experience, ‘pdf’ or ‘epsc’ is recommended for vector graphics and ‘png’ or ‘tif’ for bitmaps

  • if this command is missing, plots are not saved

sitescan, sitescan!

Spectroscopic-labeling site scans.

sitescan label entity outname [restypes [minrotamers [minpartf [chains]]]]
Arguments
  • label - label, see Rotamer libraries for list of available labels

  • entity - entity identifier specified in any of the input commands

  • outname - file name for the site scan list output, extension is .lst

  • restypes - string of single-letter identifiers of residues to be considered, optional, defaults to ‘CILMSTV’

  • minrotamers - minimum number of rotamers for a site to be considered, optional defaults to 1

  • minpartf - minimum partition function, optional, defaults to 0.1

  • chains - restrict site scan to certain chains, string, such as ‘AC’, optional, defaults to ‘*’ (all chains)

Remarks
  • argument order matters, use defaults for earlier arguments, if you wish to deviate from a default in a later argument

  • command sitescan considers only the first conformer in an ensemble, use sitescan! to scan all conformers

pairlist, pairlist!

Find feasible site pairs from site scan lists.

pairlist sitescan entity outname [rmin [rmax]]
Arguments
  • sitescan - file name of a site scan list, generated, e.g., by the sitescan keyword, extension .lst

  • entity - entity identifier specified in any of the input commands

  • outname - file name for the site scan list output, extension is .lst

  • rmin - minimum mean distance (Å) for a site pair to be considered, optional, defaults to 20 Å

  • rmax - maximum mean distance (Å) for a site pair to be considered, optional, defaults to 60 Å

Remarks
  • argument order matters, use defaults for earlier arguments, if you wish to deviate from a default in a later argument

  • command pairlist considers only pairs within the same conformer of an ensemble, use pairlist! to include inter-conformer pairs in computation of the distribution

  • the label type is taken from the site scan list

  • use hetpairlist or hetpairlist! if you want to combine sites with different labels

hetpairlist

Find feasible site pairs from two site scan lists obtained for different labels (spectroscopically orthogonal labeling).

hetpairlist sitescan_1 sitescan_2 entity outname [rmin [rmax]]
Arguments
  • sitescan_1 - file name of the first site scan list, generated, e.g., by the sitescan keyword, extension .lst

  • sitescan_2 - file name of the second site scan list

  • entity - entity identifier specified in any of the input commands

  • outname - file name for the site scan list output, extension is .lst

  • rmin - minimum mean distance (Å) for a site pair to be considered, optional, defaults to 20 Å

  • rmax - maximum mean distance (Å) for a site pair to be considered, optional, defaults to 60 Å

Remarks
  • argument order matters, use defaults for earlier arguments, if you wish to deviate from a default in a later argument

  • command hetpairlist considers only pairs within the same conformer of an ensemble, use hetpairlist! to include inter-conformer pairs in computation of the distribution

  • the label types are taken from the site scan lists

hetpairlist sitescan_1 sitescan_2 entity outname [rmin [rmax]]

distributions

Compute, save, and plot distance distributions for directly specified site pairs or pair lists. This is a block key.

distributions labels entity outname
   'address_1' 'address_2'
   []
   'pairlist'
.distributions
Arguments
  • labels - label or labels for directly specified site pairs, see Rotamer libraries for list of available labels

  • entity - entity identifier specified in any of the input commands

  • outname - basis file name for the output distributions and plots

  • address_1 - MMMx residue address for first site

  • address_2 - MMMx residue address for second site

  • pairlist - file name of a site pair list obtained by commands pairlist or hetpairlist

Remarks
  • in the block you can specify as many site pairs and pair lists as you wish

  • labels specified in the pair list(s) prevail over labels specified in the command, if these are inconsistent, it is reported in the log file

  • if the same label is used at both sites, just provide this one; for orthogonal labeling, use the syntax label_1|label_2

  • if residue addresses do not contain a conformer specification, the distribution corresponds to all conformers

trivariate

Compute and save trivariate distance distributions and plot their 2D and 1D sum projections for site triples. This is a block key.

trivariate labels entity outname
   'address_1' 'address_2' 'address_3'
   []
.trivariate
Arguments
  • labels - label or labels for specified site triples, see Rotamer libraries for list of available labels

  • entity - entity identifier specified in any of the input commands

  • outname - basis file name for the output distributions and plots

  • address_1 - MMMx residue address for first site

  • address_2 - MMMx residue address for second site

  • address_3 - MMMx residue address for third site

Remarks
  • in the block you can specify as many site triples as you wish

  • if the same label is used at both sites, just provide this one; for orthogonal labeling, use the syntax label_1|label_2|label_3

  • output is large and thus in a binary Matlab file, variables are ‘trivariate’ for the 3D array and r_axis_1, ‘r_axis_2’, ‘r_axis_3’ for the three distance axes

  • sequence of dimensions is ‘site1-site2’, ‘site1-site3’, ‘site2-site3’

  • use ‘scipy.io.loadmat’ from the SciPy library for importing to Python

ENMpairs

Score site pairs for elastic network modeling.

ENMpairs sitescan entity outname [rmin [rmax]]
Arguments
  • sitescan - file name of a site scan list, generated, e.g., by the sitescan keyword, extension .lst

  • entity - entity identifier specified in any of the input commands

  • outname - file name for the site scan list output, extension is .lst

  • rmin - minimum mean distance (Å) for a site pair to be considered, optional, defaults to 20 Å

  • rmax - maximum mean distance (Å) for a site pair to be considered, optional, defaults to 60 Å

Remarks
  • the output pair list is ordered by a score that predicts sensitivity of the pair to motion along the normal modes of the elastic network model

  • the input entity should be a single conformer, for an ensemble, only the first conformer is considered

  • the label type is taken from the site scan list

ENMpairs

Score site pairs for elastic network modeling.

ENMpairs sitescan entity outname [rmin [rmax]]
Arguments
  • sitescan - file name of a site scan list, generated, e.g., by the sitescan keyword, extension .lst

  • entity - entity identifier specified in any of the input commands

  • outname - file name for the site scan list output, extension is .lst

  • rmin - minimum mean distance (Å) for a site pair to be considered, optional, defaults to 20 Å

  • rmax - maximum mean distance (Å) for a site pair to be considered, optional, defaults to 60 Å

Remarks
  • the output pair list is ordered by a score that predicts sensitivity of the pair to motion along the normal modes of the elastic network model

  • the input entity should be a single conformer, for an ensemble, only the first conformer is considered

  • the label type is taken from the site scan list

RBreference

Finds optimal reference sites in a rigid body by maximizing the area of the triangle spanned by three sites.

RBreference entity rmin rmax sitescan_1 [sitescan_2 ...]
Arguments
  • entity - entity identifier specified in any of the input commands

  • rmin - minimum mean distance (Å) for a site pair to be considered

  • rmax - maximum mean distance (Å) for a site pair to be considered

  • sitescan_1 - file name of a site scan list, generated, e.g., by the sitescan keyword, extension .lst

  • sitescan_2 ... - optional file name(s) of further site scan lists, specify as many as you wish

Remarks
  • the output is provided in the log file in a format that can be used as input for the Rigi module

  • possibly, further chains contributing to the rigid body need to be added by the user

  • see demo_RBreference.mcx for an example