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. Bare templates can also be prepared from AlphaFold predictions downloaded from the AlphaFold Protein Structure Database by UniProt identifier with the Rigi keyword in ExperimentDesign

The following keywords are supported:

ddr

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

ddr label_1 [label_2]
   'address_1' 'address_2' 'rmean' 'rstd' [@'fname']
   ...
.ddr

Arguments

• label_1, label_2 - label types, e.g. ,

• address_1, address_2 addresses of the two labelled sites, e.g., ,

• rmean mean distance in Angstroem, e.g.

• rstd standard deviation in Angstroem, e.g.

• 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

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

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 after 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

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 parallel blocks (ceiling of number of trials divide by 10000)

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 clustered to M models

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

• the default is 20,000

• depending on memory size, clustering of a large number of models may fail, set maxtrials so that no more than 50000 trials are successful

nlink

Nucleotide link. This is a block key with lines for links.

nlink
   'address_1' 'address_2' 'nucleotides' 'length'
   ...
.nlink

Arguments

• address_1, address_2 addresses of the two anchor nucleotides, e.g., ,

• nucleotides linker segments, number of missing nucleotides + 1

• length maximum length in Angstroem, up to 6*nucleotides

Remarks

• the anchor nucleotides must exist in rigid bodies

• slightly shorter lengths, e.g. 16 instead of 18 for two missing nucleotides, improve success rate of FlexRNA, but may miss solutions with strongly extended RNA

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

plink

Peptide link. This is a block key with lines for links.

plink
   'address_1' 'address_2' 'residues' 'length'
   ...
.plink

Arguments

• address_1, address_2 addresses of the two anchor residues, e.g., ,

• residues linker segments, number of missing residues + 1

• length maximum length in Angstroem, up to 3.8*residues

Remarks

• the anchor residues must exist in rigid bodies

• slightly shorter lengths improve success rate of Flex, but risk missing conformers with strongly extended peptide linkers

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

rbtemplate

Input of a rigid-body template file.

rbtemplate file

Arguments

• file - PDB file name, must include extension , 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

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

rigid

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

• address_1 address of the first reference point, e.g.,

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

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

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 saved to MMMx_rigi.mat

• this is particularly convenient if you want to run Flex afterwards with several different restraint sets

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

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

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 little experience what is appropriate for flexible systems

• the key has no effect if no crosslinks are specified

xlink

Crosslink. This is a block key with lines for links.

xlink
   'address_1' 'address_2' 'distance'
   ...
.xlink

Arguments

• address_1, address_2 addresses of the two crosslinked residues

• distance maximum distance between CA atoms for the crosslink deemed to be possible

Remarks

• the crosslinked residues must exist in rigid bodies

• only a certain percentage of crosslinks needs to be fulfilled for the RBA to be valid, default is 30%

• use ‘xlink_percentage’ to set this percentage

• this feature is not well tested

• it is hard to predict which percentage of crosslinks should be fulfilled in any given arrangement

• it may be better to use cross-link restraints for validation of the final ensemble model