Flex¶

This module generates peptide linkers with partial or no secondary structure.

Flex can have input arguments:

!flex [coverage [models [maxtime]]]

Arguments

coverage - controls fraction of conformation space covered by the ensemble, defaults to 0.5
models - number of models per input conformer, defaults to 1
maxtime - maximum time spent on one model, defaults to 1 h

Remarks

coverage is not rigorously defined, but only an empirical control parameter
the larger coverage is, the broader is the ensemble
change default of coverage only if you have very good reasons
note that total maximum time can be as long as the product of $maxtime$ abd the number of input conformers

The following keywords are supported:

`a_prop`¶

Definition of $\alpha$ -helix propensities. This is a block key with $n$ lines for $n$ restraints.

a_prop
   'resnum' 'propensity'
   ...
.a_prop

Arguments

resnum - residue number, e.g. $120$
propensity - $\alpha$ -helical propensity, number between 0 (none) and 1 (always $\alpha$ -helical)

Remarks

secondary structure propensities can be specified only for residues in the newly generated peptide
$\alpha$ -helical propensity is realized by imposing backbone dihedrals $\psi$ and $\phi$ corresponding to $\alpha$ -helical structure

`acceptance`¶

Controls acceptance threshold.

acceptance threshold [mode]

Arguments

threshold - fraction of models that should be accepted
mode - acceptance mode, can be ‘uniform’ or ‘individual’, default is ‘uniform’

Remarks

this option requires that full distance distributions are used as restraints
with the acceptance key switches, a variant of von-Neumann rejection sampling is used
by default, Gaussian restraints are used even if full distributions are provided
the higher $threshold$ is, the faster is model generaton, but the worse is agreement of the raw ensemble with distance distributions
use higher $threshold$ if model yield is too low for the downstream part of the pipeline

`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
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

`b_prop`¶

Definition of $\beta$ -strand propensities. This is a block key with $n$ lines for $n$ restraints.

b_prop
   'resnum' 'propensity'
   ...
.b_prop

Arguments

resnum - residue number, e.g. $147$
propensity - $\beta$ -strand propensity, number between 0 (none) and 1 (always $\beta$ -strand)

Remarks

secondary structure propensities can be specified only for residues in the newly generated peptide
$\beta$ -strand propensity is realized by imposing backbone dihedrals $\psi$ and $\phi$ corresponding to $\beta$ -strand structure

`c_anchor`¶

C-terminal anchor residue for the peptide chain

c_anchor address

Arguments

address - MMMx residue address, such as ‘(D)121’

Remarks

the addressed residue must exist in the input conformers and must be a native amino acid
in pipelines with consecutive Flex modules, address is affected by automatic chain identifier changes when chains are concatenated by linkers

`c_prop`¶

Definition of cis-propensities. This is a block key with $n$ lines for $n$ restraints.

c_prop
   'resnum' 'propensity'
   ...
.c_prop

Arguments

resnum - residue number, e.g. $211$
propensity - cis-propensity, number between 0 (always trans) and 1 (always cis)

Remarks

cis-propensities can be specified only for residues in the newly generated peptide
cis-propensity is realized by imposing backbone dihedral $\omega = 0^\circ$ corresponding to a cis-residue
cis conformation usually occurs only for proline residues

`clashtest`¶

Number of generated residues after which intermediate clashtests are performed

clashtest spacing

Arguments

spacing - spacing between intermediate clashtests during backbone generation, defaults to 10000 (practically never)

Remarks

change default only if you suspect a problem that can be solved this way
usually, intermediate clashtests slow down model generation

`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
if a residue is in the newly generated peptide, use only the residue number as its address
the file name is optional, full distributions can be used
if a full distribution is provided, rmean and rstd can be skipped, these parameters are then automatically computed from the distribution
for monomodal distributions, the advantage of using full distributions in terms of ensemble quality is (at best) minor
using full distributions provides more convenient control over model yield with the ‘acceptance’ keyword

`depth`¶

Definition of bilayer immersion depth restraints. This is a block key with $n$ lines for $n$ restraints.

depth label
   'resnum' 'rmean' 'rstd'
   ...
.depth

Arguments

label - label types, e.g. $CA$ for Calpha
resnum - residue number of the site, e.g., $3$
rmean mean distance from bilayer central plane in Angstroem, e.g. $20$
rstd standard deviation if the distribution in Angstroem, e.g. $15.5$
fname file name of the distance distribution

Remarks

input structures must be in a frame where the bilayer normal is the z axis, use Prepare
use $CA$ as label identifier if you are unsure
use separate ‘depth’ blocks for different labels
depth restraints can be specified only for sites in the newly generated peptide
use a negative argument instead of $rmean$ for specifying a lower bound
use a negative argument instead of $rstd$ for specifying an upper bound

`expand`¶

Input and expansion of rigid-body arrangements.

expand [file]

Arguments

file - optional fle name for rigid-body arrangements

Remarks

without input argument, 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 for processing of Rigi results by Flex

`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

`loose`¶

Switches off sidechain clash test

loose

Remarks

this option is intended only for cases where model generation is extremely slow or impossible otherwise
do not use models obtained with the $loose$ option without subsequent refinement (e.g. using YasaraRefine)
models may clash so strongly that refinement with other programs fails

`n_anchor`¶

N-terminal anchor residue for the peptide chain

n_anchor address

Arguments

address - MMMx residue address, such as ‘(A)89’

Remarks

the addressed residue must exist in the input conformers and must be a native amino acid
in pipelines with consecutive Flex modules, address is affected by automatic chain identifier changes when chains are concatenated by linkers

`oligomer`¶

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

oligomer label n
   'resnum' 'rmean' 'rstd' [@'fname']
   ...
.oligomer

Arguments

label - label types, e.g. $ia-proxyl$
n - number of symmetry-related protomers in the oligomer, e.g. $3$
resnum - residue number of the site, e.g. $7$
rmean mean distance in Angstroem, e.g. $32.5$
rstd standard deviation in Angstroem, e.g. $15.5$
fname file name of the distance distribution

Remarks

input structures must be in a frame where the Cn symmetry axis is the z axis, use Prepare
use separate ‘oligomer’ blocks for different labels
oligomer restraints can be specified only for sites in the newly generated peptide
the file name is optional, full distributions can be used
the use of full distributions is implemented, but has not yet been tested in detail

`parallel`¶

Controls parallelization of conformer generation.

parallel trials

Arguments

trials - number of trials computed in parallel before analysis, defaults to 100

Remarks

change default only if you have a very good reason

`save`¶

Specifies basis name for saving output conformers

save file [[pdb_id] chain_id]

Arguments

file - basis file name
pdb_id - optional four-letter (pseudo) PDB identifier
chain_id - optional chain identifier

Remarks

‘_i%i_m%i.pdb’ is appended to the basis file name, the first ‘%i’ is input conformer number, the second ‘%i’ is the model number for this input
if a chain identifier is provided, a free-standing peptide gets this identifier

`scwrl4`¶

Specify full SCWRL4 pathname.

scwrl4 pathname

Arguments

pathname - full path to the SCWRL4 executable

Remarks

this is required on Linux systems, where Matlab does not find SCWRL4 even if it is on the Matlab path

`sequence`¶

amino acid sequence for the peptide chain

sequence res_start res_end seq

Arguments

res_start - number of the starting residue, such as ‘90’
res_end - number of the end residue, such as ‘120’
seq - sequence in single-letter format, such as ‘RSGRGTGRGGGGGGGGGAPRGRYGPPSRRSE’

Remarks

the sequence must consist of native amino acids

`skipto`¶

Skips input conformers.

skipto first

Arguments

first - first input conformer for which models are generated

Remarks

by default, there is no skipping
this can be used after a crash or job timeout

`verbose`¶

Sets verbose mode.

verbose [trials]

Arguments

cycles - number of Monte carlo trials after which new verbose information is written to logfile

Remarks

by default, verbose is off
verbose without argument has a default of 200 trials
verbose writes time per generated model, an estimate of remaining computation time, and statistics on the reasons for failed trials

Flex¶

a_prop¶

acceptance¶

addpdb¶

b_prop¶

c_anchor¶

c_prop¶

clashtest¶

ddr¶

depth¶

expand¶

getpdb¶

loose¶

n_anchor¶

oligomer¶

parallel¶

save¶

scwrl4¶

sequence¶

skipto¶

verbose¶

`a_prop`¶

`acceptance`¶

`addpdb`¶

`b_prop`¶

`c_anchor`¶

`c_prop`¶

`clashtest`¶

`ddr`¶

`depth`¶

`expand`¶

`getpdb`¶

`loose`¶

`n_anchor`¶

`oligomer`¶

`parallel`¶

`save`¶

`scwrl4`¶

`sequence`¶

`skipto`¶

`verbose`¶