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:

`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

`distributions`¶

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

distributions labels entity outname [rmin [rmax [resolution]]]
   '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
rmin - minimum of distance axis, defaults to 10 Angstrom
rmax - maximum of distance axis, defaults to 150 Angstrom
resolution - resolution of distance axis, defaults to 0.5 Angstrom
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

`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

`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

`getAlphaFold`¶

Input of an AlphaFold prediction.

import UniProtID identifier

Arguments

UniProtID - UniProt identifier for the AlphaFold prediction
identifier - module-internal entity identifier of this ensemble

Remarks

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

`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

`hetpairlist`, `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]]

`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

`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

`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

`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

`RigiFlex`¶

Prepare RigiFlex rigid-body file and MMMx script template from AlphaFold prediction

RigiFlex UniProtID

Arguments

UniProtID - sequence ID from UniProt, for which a prediction exists in the AlphaFold Protein Structure Database

Remarks

output file names are automatically generated from the UniProt ID
if no prediction exists in the database, no output is generated and an error message is written to the log file
the task also prepares spin-labelling site scan lists for all detected folded domains

`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

`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

ExperimentDesign¶

addpdb¶

distributions¶

ENMpairs¶

expand¶

getAlphaFold¶

getens¶

hetpairlist, hetpairlist!¶

import¶

pairlist, pairlist!¶

plot¶

RBreference¶

RigiFlex¶

sitescan, sitescan!¶

trivariate¶

`addpdb`¶

`distributions`¶

`ENMpairs`¶

`expand`¶

`getAlphaFold`¶

`getens`¶

`hetpairlist`, `hetpairlist!`¶

`import`¶

`pairlist`, `pairlist!`¶

`plot`¶

`RBreference`¶

`RigiFlex`¶

`sitescan`, `sitescan!`¶

`trivariate`¶