Rigi

This module generates ensembles of rigid-body arrangements. Sequence of commands is irrelevant.

Features are demonstrated in example demo_Rigi.mcx, which uses module Prepare to generate a rigid-body template from a structure downloaded from the PDB server.

The following keywords are supported:

rbtemplate

Input of a rigid-body template file.

rbtemplate file
Arguments
  • file - PDB file name, must include extension .pdb, otherwise download from the PDB server is attempted

Remarks
  • the command addpdb is synonymous with rbtemplate

  • you can use the merge command in module Prepare to generate a rigid-body template file

rigid

Definition of rigid bodies. This is a block key with n lines for n rigid bodies.

rigid chain_1 [chain_2 ...]
   'address_1' 'label_1'
   'address_2' 'label_2'
   'address_3' 'label_3'
.rigid
Arguments
  • chain_1, chain_2, … - chains belonging to this rigid body, example (A) (B)

  • address_1 address of the first reference point, e.g., (A)16

  • label_1 label type for the first reference point, e.g. mtsl

Remarks
  • use exactly three reference points

  • at least one chain and as many chains as needed can belong to one rigid body

  • reference point addresses mus be in one of the chains that belong to the rigid body

  • you can define as many rigid bodies as you need, but computational effort increases exponentially

  • there must be at least two rigid bodies

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, (D)148

  • 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
  • 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, full distributions are not currently used

maxtrials

Maximum number of trials in exhaustive search.

maxtrials T
Arguments
  • T - maximum number of trials, determines, how long an exhaustive search takes

Remarks
  • this must be specified, start with 10,000 if you are not sure and see how long it takes

  • actual number of trials is a product of integer digital resolutions for all core restraints and may be smaller

  • the larger T, the better the resolution of the exhaustive search

  • computation time is linear in actual number of trials

maxtime

Maximum run time in hours.

maxtime t
Arguments
  • t - approximate maximum run time allowed for Rigi

Remarks
  • computation can take somewhat longer, because runtime ist tested only execution of full parallel blocks (10,000 trials)

  • if Rigi is interrupted by timeout, sampling is not exhaustive

  • for production runs, reduce maxtrials until you can complete the exhaustive sampling in a reasonable time

  • default is 48 h

models

Maximum number of rigid-body arrangements in output.

models M
Arguments
  • M - maximum number of models that are returned

Remarks
  • if exhaustive sampling yields less models, this setting has no effect

  • if exhaustive sampling yields more models, the solutions are hierarchically cluster to M models

  • use this, if Rigi returns too many models for further processing

  • the default is 20,000

xl_percentage

Specifies the percentage of crosslink restraints that must be fulfilled for an RBA to be accepted

xl_percentage p
Arguments
  • p - number between 0 and 100, defaults to 30%

Remarks
  • there is few experience what is appropriate for flexible systems

  • directive has no effect, if no crosslinks are specified

separate off

Turn off automatic separation of rigid bodies in the template file.

Arguments
  • none, separate off is the only syntax that has an influence

Remarks
  • do this only if the rigid bodies are already well separated in the template

  • if you wish to superimpose the ensemble onto a template, this is better done in module EnsembleAnalysis

superimpose

Superimpose all rigid-body arrangements at one rigid body.

superimpose rigid_body
Arguments
  • rigid_body - number of the rigid body at which arrangments are superimposed

Remarks
  • the number corresponds to the sequence of rigid blocks in the control file

save

Specifies name for saving the output in MMMx:rigid_body format.

save fname
Arguments
  • fname - file name for output, extension .mat is appended if none

Remarks
  • if not present, output is automatically save to MMMx_rigi.mat

savepdb

Specifies basis name for saving individual rigid-body arrangements to PDB files

savepdb bname
Arguments
  • bname - basis file name for PDB files, _rba_%i.pdb is appended, where %i denotes the number of the RBA

Remarks
  • if not present, no individual PDB files are saved

maxsize

Specifies the maximum size (extension) of a rigid-body arrangement

maxsize size
Arguments
  • size - maximum distance between reference points in a rigid-body arrangement, defaults to 180 Angstroem

parallel

Specifies number of trials in a parallel block

parallel ptrials
Arguments
  • ptrials - number of trials performed in parallel, defaults to 10,000

Remarks
  • change from default only if you have a very good reason

probability

Specifies the probability covered by the RBA ensemble

probability p
Arguments
  • p - number between 0 and 1, defaults to 0.5

Remarks
  • change from default only if you have a very good reason

resolution

Sets a resolution limit for the exhaustive search of RBA arrangement space

resolution res
Arguments
  • res - resolution in Angstroem, defaults to 3 Angstroem

Remarks
  • actual resolution can be larger, but not smaller

  • do not change from default, if you are not sure