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:

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

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

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

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

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

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

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

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

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

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

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_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

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

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

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

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

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