ENM

This module generates ensembles from a known structure template of a protein or complex by deforming an elastic network model of the backbone to fit restraints.

getpdb

Input of a raw ensemble (uniform populations) by reading a single PDB file.

getpdb file
Arguments
  • file - file name or PDB identifier, must have extension ‘.pdb’ if it specifies a file

Remarks
  • the PDB file can contain several models (conformers) or a single one, by default, the first conformer is used

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
  • ‘_m%i.pdb’ is appended to the basis file name, where ‘%i’ is the output model number

conformer

Specifies input conformer from an input ensemble.

conformer number
Arguments
  • number - conformer number

Remarks
  • if the key is missing, the first conformer is used

remove

Removes a residue from the template.

remove address
Arguments
  • address - MMMx address of the residue to be removed

Remarks
  • this can be used for removing cofactors of a template for fitting an apo structure

  • use several remove keys if you wish to remove more than one residue

  • for more complex manipulation of the template, use the Prepare module

chains

Use only some of the chains from the input structure.

chains chain_id_1 [chain_id_2 ...]
Arguments
  • chain_id_1 - chain identifier of a chain to the included. e.g. ‘A’

  • chain_id_2 ... - optional chain identifiers of additional chains to the included. e.g. ‘B’ ‘C’

Remarks
  • this can be used if the template is a complex and the target is one of its components

  • there should be only one chains key or none at all

  • by default, all chains are included in the template

drag

Definition of residues dragged along with the elastic network. This is a block key with n lines for n residues.

drag
   'address'
   ...
.drag
Arguments
  • address - address of a residue to be dragged along, e.g. (A)501

Remarks
  • by default, only peptide chains are converted to a C\alpha elastic network model and deformed

  • dragged residues are subjected to the same rotation and translation as the closest C\alpha atom

  • use this for ions and other cofactors

  • it is advisable to refine the models afterwards

ensemble

Specifies size of the output ensemble

ensemble size [uncertainty]
Arguments
  • size - number of models in the output ensemble, defaults to 100

  • uncertainty - optional uncertainty threshold, multiplier to standard deviation, defaults to 3

Remarks
  • ‘_m%i.pdb’ is appended to the basis file name, where ‘%i’ is the output model number

  • default uncertainty assumes subsequent ensemble fitting and contraction, use a lower value, if this is not intended

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 RNA, 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

  • distance distribution restraints are always treated as full distribution, if only rmean and rstd are provided, the distance is computed * test of distance distribution restraints is done with full models and based on the overlap metric