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.

Some keywords are provided for selecting part of an input structure. If you need to modify an input structure more extensively, please 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

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

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 ‘deer’ 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

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

getAlphaFold

Input of an AlphaFold prediction.

getAlphaFold UniProtID
Arguments

  • UniProtID - UniProt identifier for the AlphaFold prediction

Remarks

  • note that not all proteins in UniProt have AlphaFold predictions in the database

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

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

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