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 ['protons']
- Arguments
file
- file name, can contain wildcardsprotons
- if directive ‘protons’ is present, protons from the input file are kept
- Remarks
use wildcard ‘*’ for part of the filename to process all conformers from a previous step in the pipeline
without any input, Flex generates free peptide chains
use this command for attaching flexible peptide chains or linkers to existing structures
in pipelines, use this command after previous Flex or FlexRNA modules
by default, protons are removed in order to avoid ensemble inconsistency arising from different protonation states of individual conformers
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
getpdb
¶
Input of a raw ensemble (uniform populations) 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
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’
ddr
¶
Definition of distance distribution restraints. This is a block key with lines for
restraints.
ddr label_1 [label_2]
'address_1' 'address_2' 'rmean' 'rstd' [@'fname']
...
.ddr
- Arguments
label_1
,label_2
- label types, e.g.,
address_1
,address_2
addresses of the two labelled sites, e.g.,,
rmean
mean distance in Angstroem, e.g.rstd
standard deviation in Angstroem, e.g.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
andrstd
can be skipped
pre
¶
Definition of NMR paramagnetic relaxation enhancement (PRE) restraints as intensity ratios. This is a block key with lines for
restraints.
pre label larmor td R2dia [taui [taur [maxrate]]]
'address_1' 'ratio' ['std']
...
.pre
- Arguments
label
- label type, e.g.larmor
- proton Larmor frequency in MHz, e.g. 700td
- total INEPT delay in ms. e.g. 10.8R2dia
- relaxation rate for the diamagnetic sample in, e.g. 66
taui
- correlation time of internal label motion in ns, e.g. 0.6, default 0.5taur
- rotational correlation time of the protein in ns, e.g. 3.7maxrate
- maximum rate enhancement in, e.g. 150, defaults to 170
address
- site address, e.g.,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 . This is a block key with
lines for
restraints.
prerates label larmor td R2dia [taui [taur [maxrate]]]
'address_1' 'rate' ['std']
...
.prerates
- Arguments
label
- label type, e.g.larmor
- proton Larmor frequency in MHz, e.g. 700td
- total INEPT delay in ms. e.g. 10.8R2dia
- relaxation rate for the diamagnetic sample in, has no effect for rate fitting
taui
- correlation time of internal label motion in ns, e.g. 0.6, default 0.5taur
- rotational correlation time of the protein in ns, e.g. 3.7maxrate
- maximum rate enhancement in, e.g. 150, defaults to 170
address
- site address, e.g.,rate
- rate enhancement in, 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 packageresolution
- 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
- 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
plotgroup
¶
Assigns conformers to plot groups.
plotgroup svgcolor conformers
- Arguments
svgcolor
- a scalable vector graphics color name for the distributions of the subensembleconformers
- 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’