Locate

This module computes a probability density that locates a spectroscopic label with respect to a resolved part of a structure.

Locate can have an input argument:

!locate [coverage]
Arguments

  • coverage - probability covered by an isosurface, defaults to 0.5

Remarks

  • the density level corresponding to this isosurface is written to the logfile

cube

Specifies edge length of the density cube

cube size
Arguments

  • size - edge length of the density cube in Angstroem, cube volume is size \times size \times size, default is 75

Remarks

  • the most probable location defines the cube center

  • the largest relative probability density at a cube border is reported in the logfile

  • if there is high relative probability density at the cube edges with the default values, the location is very poorly restrained

getAlphaFold

Input of a template by reading an AlphaFold prediction from the database.

getAlphaFold UniProtID
Arguments

  • UniProtID - UniProt identifier of the AlphaFold prediction

Remarks

  • note that not all proteins in UniProt may have an AlphaFold prediction in the database

getpdb

Input of a template by reading a single local PDB file or retrieving a PDB structure from a server.

getpdb file
Arguments

  • file - file name or PDB identifier, must have extension ‘.pdb’ if it specifies a file

Remarks

  • if the template has several conformers, the first one is used

grid

Specifies number of grid points along one dimension of the density cube

grid size
Arguments

  • size - number of grid points along one dimension, grid size is size \times size \times size, default is 176

Remarks

  • memory and computation time scale with size^3

reference

Definition of distance distribution restraints to reference points. This is a block key with n lines for n reference points.

reference label
   address 'rmean' 'rstd' [@'fname']
   ...
.reference
Arguments

  • label - label type, e.g. mtsl

  • address - address of the reference point, e.g., (A)75

  • rmean mean distance in Angstroem, e.g. 32.7

  • rstd standard deviation in Angstroem, e.g. 3.9

  • fname optional file name of the distance distribution

Remarks

  • use separate ‘reference’ blocks for different label types

  • the file name is optional, full distributions can be used

  • if a full distribution is provided, rmean and rstd can be skipped

save

Specifies basis name for saving output conformers

save file
Arguments

  • file - file name for output density cube file

Remarks

  • extension ‘.mat’ is appended if there is none, use extension ‘.mat’ for MMMx density files or ‘.mrc’ for MRC files