EnsembleFit¶

This module performs integrative fitting of a raw ensemble to various sets of experimental restraints. The ensemble is contracted by fitting populations and discarding conformers with zero or very low population.

`addpdb`¶

Input of template conformers from PDB files.

addpdb file

Arguments

file - file name, can contain wildcards

Remarks

use wildcard ‘*’ for part of the filename to process all conformers from a previous step in the pipeline
use this command to generate a raw ensemble or add conformers to a raw ensemble generated by getpdb
only one addpdb directive is allowed (the last one overwrites previous ones)

`expand`¶

Input and expansion of rigid-body arrangements.

expand [fname]

Arguments

file - optional fle name for saving extracted rigid-body arrangements

Remarks

the output of a previous Rigi module in the pipeline is expanded
input file format is the Matlab output format of Rigi
use this command only for direct processing of Rigi results by EnsembleFit * this keyword cannot be combined with initial, addpdb, and getpdb
only one expand directive is allowed (the last one overwrites previous ones)

`getpdb`¶

Input of a raw ensemble by reading a single PDB file.

getpdb file

Arguments

file - file name

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, otherwise populations are uniform
only one getpdb directive is allowed (the last one overwrites previous ones)

`initial`¶

Input an initial ensemble with populations from an MMMx ensemble fle

initial file

Arguments

file - file name, must refer to a single ensemble

Remarks

use this in combination with nofit to generate plots or save data for an existing ensemble
it is possible to combine initial with addpdb and/or getpdb
only one initial directive is allowed (the last one overwrites previous ones)

`save`¶

Specifies basis name for saving output conformers

save file

Arguments

file - output file name, extension should be ‘.ens’

Remarks

if the save key is missing, the ensemble list is saved to ‘ensemble.ens’

`csv`¶

Save fit results to comma-separated value (CSV) files

csv

Remarks

by default, full fit results are saved only to a Matlab file and CSV saving is off
if csv is on, all information underlying fit plots is saved, even if plot is off
this feature also reports fit quality of individual restraints to the logfile (except PRE)
small-angle scattering data has four columns: scattering vector, intensity, standard deviation, fitted intensity
PRE data has four columns: index, experimental PRE ratio rate, standard deviation, fitted PRE ratio or rate
distance distribution restraint (ddr) data has a variable column format, the format is specified in the logfile for each individual restraint
specifiers for ddr columns are: r distance axis, d experimental distribution, l lower bound, u upper bound, f fitted distribution, g distribution corresponding to a Gaussian restraint
if plotgroups were specified for ddr, a format specifier s1 stands for plot group 1, s2 for plot group 2, and so on

`ddr`¶

Definition of distance distribution restraints. This is a block key with $n$ lines for $n$ restraints.

ddr label_1 [label_2]
   'address_1' 'address_2' 'rmean' 'rstd' [@'fname']
   ...
.ddr

Arguments

label_1, label_2 - label types, e.g. $mtsl$ , $dota-gd$
address_1, address_2 addresses of the two labelled sites, e.g., $(A)16$ , $107$
rmean mean distance in Angstroem, e.g. $32.5$
rstd standard deviation in Angstroem, e.g. $15.5$
fname optional file name of the distance distribution

Remarks

if both labels are the same, it is sufficient to specify the label type once
use separate ‘ddr’ blocks for each label combination
the file name is optional, but using full distributions is strongly recommended
if a full distribution is provided, rmean and rstd can be skipped

`pre`¶

Definition of NMR paramagnetic relaxation enhancement (PRE) restraints as intensity ratios. This is a block key with $n$ lines for $n$ restraints.

pre label larmor td R2dia [taui [taur [maxrate]]]
   'address_1' 'ratio' ['std']
   ...
.pre

Arguments

label - label type, e.g. $mtsl$
larmor - proton Larmor frequency in MHz, e.g. 700
td - total INEPT delay in ms. e.g. 10.8
R2dia - relaxation rate for the diamagnetic sample in $s^{-1}$ , e.g. 66
taui - correlation time of internal label motion in ns, e.g. 0.6, default 0.5
taur - rotational correlation time of the protein in ns, e.g. 3.7
maxrate - maximum rate enhancement in $s^{-1}$ , e.g. 150, defaults to 170
address - site address, e.g., $(A)16$
ratio - intensity ratio between paramagnetic and diamagnetic sample, should be between 0 and 1 * std - standard deviation of the PRE ratio, optional

Remarks

ratios above 1 are accepted and interpreted as no PRE effect
‘taui’ may be estimated from the CW EPR spectrum of the labelled sample
‘taur’ will be estimated or computed with HYDROPRO if it is not provided
for disordered systems, a general ‘taur’ for all conformers may be a poor approximation
if standard deviation is missing, all PRE restraints in this block have the same weight

`prerate`¶

Definition of NMR paramagnetic relaxation enhancement (PRE) restraints as relaxation enhancement rates $\Gamma_2$ . This is a block key with $n$ lines for $n$ restraints.

prerates label larmor td R2dia [taui [taur [maxrate]]]
   'address_1' 'rate' ['std']
   ...
.prerates

Arguments

label - label type, e.g. $mtsl$
larmor - proton Larmor frequency in MHz, e.g. 700
td - total INEPT delay in ms. e.g. 10.8
R2dia - relaxation rate for the diamagnetic sample in $s^{-1}$ , has no effect for rate fitting
taui - correlation time of internal label motion in ns, e.g. 0.6, default 0.5
taur - rotational correlation time of the protein in ns, e.g. 3.7
maxrate - maximum rate enhancement in $s^{-1}$ , e.g. 150, defaults to 170
address - site address, e.g., $(A)16$
rate - rate enhancement in $s^{-1}$ , e.g. 40 * std - standard deviation of the rate enhancement, optional

Remarks

ratios above 1 are accepted and interpreted as no PRE effect
‘taui’ may be estimated from the CW EPR spectrum of the labelled sample
‘taur’ will be estimated or computed with HYDROPRO if it is not provided
for disordered systems, a general ‘taur’ for all conformers may be a poor approximation
if standard deviation is missing, all PRE restraints in this block have the same weight

`sans`¶

Specifies basis name for saving output conformers

sans data [resolution [deuteration]]

Arguments

data - name of the input scattering data file, must be a file acceptable by ‘cryson’ in the ATSAS package
resolution - name of a resolution file, must be a file acceptable by ‘cryson’ in the ATSAS package * deuteration - fraction of buffer deuteration, between 0 and 1, e.g. 0.66, optional

Remarks

SANS fitting works without resolution file, but it is strongly recommended to provide one
if deuteration is not specified, natural proton abundance buffer is assumed
SANS curves are computed by the ATSAS package installed on this computer and present on the Matlab path

`saxs`¶

Specifies basis name for saving output conformers

saxs data ['crysol3']

Arguments

data - name of the input scattering data file, must be a file acceptable by ‘crysol’ in the ATSAS package
'crysol3' - if crysol3 is specified, SAXS data are computed with this newer version

Remarks

crysol3 uses a different algorithm for the hydration shell
fitting once with original crysol and once with crysol3 can provide an idea about uncertainty due to hydration shell modelling
SAXS curves are computed by the ATSAS package installed on this computer and present on the Matlab path

`nofit`¶

Specifies basis name for saving output conformers

nofit

Remarks

the key requests only restraint computation and analysis for the input ensemble, without population fitting

`rmean`¶

Specifies basis name for saving output conformers

rmean

Remarks

the key requests that mean distances instead of distance distribution restraints are fitted
do this only if you have a very good reason

`blocksize`¶

Specifies initial block size for population fitting

blocksize conformers

Arguments

conformers - initial number of conformers per block, defaults to 100

Remarks

block size is adaptive, there should be no reason to depart from the default

`interactive`¶

Specifies basis name for saving output conformers

interactive

Remarks

the key enables display of fit information in a plot during fitting
this option may be useful for tests, but should be skipped for runs on a server

`plot`¶

Specifies basis name for saving output conformers

plot

Remarks

the key generates Matlab result plots after fitting, default is not to plot
this can be useful even on a server, if you save the plots as PDF files

`figures`¶

Specifies a graphics format for saving figures.

figures format

Arguments

format - optional, one of the formats in which Matlab can save figures, e.g. ‘pdf’

Remarks

this switches on figure saving, which is off by default
in most contexts, vector graphic output as ‘pdf’ works best, this is the default
plot is switched on if it was not already switched on
file names for small-angle scattering fits are derived from the name of the input data
file names for distance distribution overlap are derived from the two site addresses
file names for PRE fits are derived from the labeling site
each small-angle scattering restraint generates four plots: linear, semi-logarithmic, double logarithmic, and residual

`plotgroup`¶

Assigns conformers to plot groups.

plotgroup svgcolor conformers

Arguments

svgcolor - a scalable vector graphics color name for the distributions of the subensemble
conformers - a conformer number list in MMMx address list format

Remarks

see SVG color table for available colors
conformer numbers are separated by comma and ranges are indicated by hyphen, e.g. ‘2, 4, 7-11, 15’

EnsembleFit¶

addpdb¶

expand¶

getpdb¶

initial¶

save¶

csv¶

ddr¶

pre¶

prerate¶

sans¶

saxs¶

nofit¶

rmean¶

blocksize¶

interactive¶

plot¶

figures¶

plotgroup¶

`addpdb`¶

`expand`¶

`getpdb`¶

`initial`¶

`save`¶

`csv`¶

`ddr`¶

`pre`¶

`prerate`¶

`sans`¶

`saxs`¶

`nofit`¶

`rmean`¶

`blocksize`¶

`interactive`¶

`plot`¶

`figures`¶

`plotgroup`¶