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 , 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 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 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 , default is 176
- Remarks
memory and computation time scale with
reference
¶
Definition of distance distribution restraints to reference points. This is a block key with lines for reference points.
reference label
address 'rmean' 'rstd' [@'fname']
...
.reference
- Arguments
label
- label type, e.g.address
- address of the reference point, e.g.,rmean
mean distance in Angstroem, e.g.rstd
standard deviation in Angstroem, e.g.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
andrstd
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