FlexRNA

This module generates single-stranded RNA linkers.

FlexRNA can have input arguments:

!flexRNA [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, FlexRNA generates free RNA chains

  • use this command for attaching single-stranded RNA chains or linkers to existing structures

  • in pipelines, use this command after previous Flex or FlexRNA modules

anchor_3p

3’-terminal anchor residue for the peptide chain

anchor_3p address
Arguments

  • address - MMMx residue address, such as ‘(C)9’

Remarks

  • the addressed nucleotide must exist in the input conformers and must be a native nucleotide

  • in pipelines with consecutive FlexRNA modules, address is affected by automatic chain identifier changes when chains are concatenated by linkers

anchor_5p

5’-terminal anchor residue for the peptide chain

anchor_5p  address
Arguments

  • address - MMMx residue address, such as ‘(B)3’

Remarks

  • the addressed nucleotide must exist in the input conformers and must be a native nucleotide

  • in pipelines with consecutive FlexRNA 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 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 completed models and based on the overlap metric

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 FlexRNA

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

nucleotide sequence for the RNA chain

sequence nt_start nt_end seq
Arguments

  • nt_start - number of the starting nucleotide, such as ‘4’

  • nt_end - number of the end residue, such as ‘8’

  • seq - sequence in single-letter format, such as ‘UUCGA’

Remarks

  • the sequence must consist of native nucleotides

verbose

Sets verbose mode.

verbose [trials]
Arguments

  • trials - number of Monte carlo trials after which new verbose information is written to logfile and command window

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 number of successful trials to the command window