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

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 superimpose

Remarks

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